What can you tell us about how you got into the situation where there were left
over certmonger trackers? Did you install and uninstall multiple times? Were
there failures in any of those? What are the contents of the request files?

IPA does tell certmonger to stop tracking certificates that it manages during a
normal uninstallation, so this would not be a regression from previous releases.

You need to start the certmonger service for ipa-getcert to work. It is
unrelated to IPA being installed/configured.

I *think* this might be related to one of the `ipa-server-install --uninstall' exiting in the middle of the uninstall process when it couldn't remove one of the files in /etc/httpd/conf.d/ 

ipa-server-install --uninstall told me that IPA is not installed, but not all the steps in the uninstall passed through. So I guess the system was somewhere in the middle and I didn't find a way to finish the uninstall. 

I'm able to reproduce this 100% by running 

1) ipa-server-install with parameters mentioned in comment #0, 


2) chattr +i /etc/httpd/conf.d/ipa.conf


3) # ipa-server-install --uninstall

This is a NON REVERSIBLE operation and will delete all data and configuration!

Are you sure you want to continue with the uninstall procedure? [no]: yes
Shutting down all IPA services
Removing IPA client configuration
Unconfiguring ntpd
Unconfiguring CA directory server
Unconfiguring CA
Unconfiguring web server
ipa         : ERROR    Error removing /etc/httpd/conf.d/ipa.conf: [Errno 1] Operation not permitted: '/etc/httpd/conf.d/ipa.conf'


Unconfiguring krb5kdc
Unconfiguring kadmin
Unconfiguring directory server
Unconfiguring ipa_memcached



4) And then re-runnning ipa-server-install again with the parameters mentioned in comment #0. 

...
[15/35]: creating indices
  [16/35]: configuring ssl for ds instance
ipa         : ERROR    Didn't get new certmonger request, got Request "20120427153912" modified.

Unexpected error - see ipaserver-install.log for details:
 certmonger did not issue new tracking request for 'NICK_REMOVED' in '/etc/dirsrv/slapd-MY_DOMAIN_REMOVED/'. Use 'ipa-getcert list' to list existing certificates.
[root@machine ~]# /etc/init.d/certmonger start
Starting certmonger:                                       [  OK  ]
[root@machine ~]# ipa-getcert list
Number of certificates and requests being tracked: 2.
Request ID '20120427153912':
        status: MONITORING
        stuck: no
        key pair storage: type=NSSDB,location='/etc/dirsrv/slapd-DOMAIN_REMOVED',nickname='NICK_REMOVED',token='NSS Certificate DB',pinfile='/etc/dirsrv/slapd-DOMAIN_REMOVED/pwdfile.txt'
        certificate: type=NSSDB,location='/etc/dirsrv/slapd-DOMAIN_REMOVED',nickname='NICK_REMOVED',token='NSS Certificate DB'
        CA: IPA
        issuer: E=ADMIN_EMAIL_REMOVED,CN="MY_COMPANY_REMOVED Certificate Authority",OU=Certificate Authority,O="MY_COMPANY_REMOVED",L=MY_CITY_REMOVED,ST=Czech Republic,C=CZ
        subject: E=ADMIN_EMAIL_REMOVED,CN=MY_FQDN_REMOVED,O="MY_COMPANY_REMOVED",ST=Czech Republic,C=CZ
        expires: 2013-04-27 07:04:20 UTC
        command: /usr/lib64/ipa/certmonger/restart_dirsrv DOMAIN_REMOVED
        track: yes
        auto-renew: yes
Request ID '20120427154011':
        status: MONITORING
        stuck: no
        key pair storage: type=NSSDB,location='/etc/httpd/alias',nickname='NICK_REMOVED',token='NSS Certificate DB',pinfile='/etc/httpd/alias/pwdfile.txt'
        certificate: type=NSSDB,location='/etc/httpd/alias',nickname='NICK_REMOVED',token='NSS Certificate DB'
        CA: IPA
        issuer: E=ADMIN_EMAIL_REMOVED,CN="MY_COMPANY_REMOVED Certificate Authority",OU=Certificate Authority,O="MY_COMPANY_REMOVED",L=MY_CITY_REMOVED,ST=Czech Republic,C=CZ
        subject: E=ADMIN_EMAIL_REMOVED,CN=MY_FQDN_REMOVED,O="MY_COMPANY_REMOVED",ST=Czech Republic,C=CZ
        expires: 2013-04-27 07:04:20 UTC
        command: /usr/lib64/ipa/certmonger/restart_httpd
        track: yes
        auto-renew: yes

Upstream ticket:
https://fedorahosted.org/freeipa/ticket/2702

Fixed upstream.

master: 102765c69fb702cd422611ef21b14b2914cee51f

ipa-3-0: 555a0eef808aafa64330a615bfa2c474e9277cba

*** Bug 862437 has been marked as a duplicate of this bug. ***

See the upstream ticket for information on testing.

Verified.

Version ::

ipa-server-3.0.0-21.el6.x86_64

Automated Test Results (manually run) ::

::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
:: [   LOG    ] :: ipaserverinstall_bz817080 - ipa-server-install --uninstall doesn't clear certmonger dirs, which leads to install failing
::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::


The log file for this installation can be found in /var/log/ipaserver-install.log
==============================================================================
This program will set up the IPA Server.

This includes:
  * Configure a stand-alone CA (dogtag) for certificate management
  * Configure the Network Time Daemon (ntpd)
  * Create and configure an instance of Directory Server
  * Create and configure a Kerberos Key Distribution Center (KDC)
  * Configure Apache (httpd)
  * Configure DNS (bind)

To accept the default shown in brackets, press the Enter key.

Warning: skipping DNS resolution of host rhel6-4.testrelm.com
The domain name has been determined based on the host name.

Using reverse zone 122.168.192.in-addr.arpa.

The IPA Master Server will be configured with:
Hostname:      rhel6-4.testrelm.com
IP address:    192.168.122.64
Domain name:   testrelm.com
Realm name:    TESTRELM.COM

BIND DNS server will be configured to serve IPA domain with:
Forwarders:    192.168.122.1
Reverse zone:  122.168.192.in-addr.arpa.

Configuring NTP daemon (ntpd)
  [1/4]: stopping ntpd
  [2/4]: writing configuration
  [3/4]: configuring ntpd to start on boot
  [4/4]: starting ntpd
Done configuring NTP daemon (ntpd).
Configuring directory server for the CA (pkids): Estimated time 30 seconds
  [1/3]: creating directory server user
  [2/3]: creating directory server instance
  [3/3]: restarting directory server
Done configuring directory server for the CA (pkids).
Configuring certificate server (pki-cad): Estimated time 3 minutes 30 seconds
  [1/21]: creating certificate server user
  [2/21]: creating pki-ca instance
  [3/21]: configuring certificate server instance
  [4/21]: disabling nonces
  [5/21]: creating CA agent PKCS#12 file in /root
  [6/21]: creating RA agent certificate database
  [7/21]: importing CA chain to RA certificate database
  [8/21]: fixing RA database permissions
  [9/21]: setting up signing cert profile
  [10/21]: set up CRL publishing
  [11/21]: set certificate subject base
  [12/21]: enabling Subject Key Identifier
  [13/21]: setting audit signing renewal to 2 years
  [14/21]: configuring certificate server to start on boot
  [15/21]: restarting certificate server
  [16/21]: requesting RA certificate from CA
  [17/21]: issuing RA agent certificate
  [18/21]: adding RA agent as a trusted user
  [19/21]: configure certificate renewals
  [20/21]: configure Server-Cert certificate renewal
  [21/21]: Configure HTTP to proxy connections
Done configuring certificate server (pki-cad).
Configuring directory server (dirsrv): Estimated time 1 minute
  [1/38]: creating directory server user
  [2/38]: creating directory server instance
  [3/38]: adding default schema
  [4/38]: enabling memberof plugin
  [5/38]: enabling winsync plugin
  [6/38]: configuring replication version plugin
  [7/38]: enabling IPA enrollment plugin
  [8/38]: enabling ldapi
  [9/38]: disabling betxn plugins
  [10/38]: configuring uniqueness plugin
  [11/38]: configuring uuid plugin
  [12/38]: configuring modrdn plugin
  [13/38]: enabling entryUSN plugin
  [14/38]: configuring lockout plugin
  [15/38]: creating indices
  [16/38]: enabling referential integrity plugin
  [17/38]: configuring ssl for ds instance
  [18/38]: configuring certmap.conf
  [19/38]: configure autobind for root
  [20/38]: configure new location for managed entries
  [21/38]: restarting directory server
  [22/38]: adding default layout
  [23/38]: adding delegation layout
  [24/38]: adding replication acis
  [25/38]: creating container for managed entries
  [26/38]: configuring user private groups
  [27/38]: configuring netgroups from hostgroups
  [28/38]: creating default Sudo bind user
  [29/38]: creating default Auto Member layout
  [30/38]: adding range check plugin
  [31/38]: creating default HBAC rule allow_all
  [32/38]: Upload CA cert to the directory
  [33/38]: initializing group membership
  [34/38]: adding master entry
  [35/38]: configuring Posix uid/gid generation
  [36/38]: enabling compatibility plugin
  [37/38]: tuning directory server
  [38/38]: configuring directory to start on boot
Done configuring directory server (dirsrv).
Configuring Kerberos KDC (krb5kdc): Estimated time 30 seconds
  [1/10]: adding sasl mappings to the directory
  [2/10]: adding kerberos container to the directory
  [3/10]: configuring KDC
  [4/10]: initialize kerberos container
  [5/10]: adding default ACIs
  [6/10]: creating a keytab for the directory
  [7/10]: creating a keytab for the machine
  [8/10]: adding the password extension to the directory
  [9/10]: starting the KDC
  [10/10]: configuring KDC to start on boot
Done configuring Kerberos KDC (krb5kdc).
Configuring kadmin
  [1/2]: starting kadmin 
  [2/2]: configuring kadmin to start on boot
Done configuring kadmin.
Configuring ipa_memcached
  [1/2]: starting ipa_memcached 
  [2/2]: configuring ipa_memcached to start on boot
Done configuring ipa_memcached.
Configuring the web interface (httpd): Estimated time 1 minute
  [1/13]: setting mod_nss port to 443
  [2/13]: setting mod_nss password file
  [3/13]: enabling mod_nss renegotiate
  [4/13]: adding URL rewriting rules
  [5/13]: configuring httpd
  [6/13]: setting up ssl
  [7/13]: setting up browser autoconfig
  [8/13]: publish CA cert
  [9/13]: creating a keytab for httpd
  [10/13]: clean up any existing httpd ccache
  [11/13]: configuring SELinux for httpd
  [12/13]: restarting httpd
  [13/13]: configuring httpd to start on boot
Done configuring the web interface (httpd).
Applying LDAP updates
Restarting the directory server
Restarting the KDC
Configuring DNS (named)
  [1/9]: adding DNS container
  [2/9]: setting up our zone
  [3/9]: setting up reverse zone
  [4/9]: setting up our own record
  [5/9]: setting up kerberos principal
  [6/9]: setting up named.conf
  [7/9]: restarting named
  [8/9]: configuring named to start on boot
  [9/9]: changing resolv.conf to point to ourselves
Done configuring DNS (named).

Global DNS configuration in LDAP server is empty
You can use 'dnsconfig-mod' command to set global DNS options that
would override settings in local named.conf files

Restarting the web server
==============================================================================
Setup complete

Next steps:
	1. You must make sure these network ports are open:
		TCP Ports:
		  * 80, 443: HTTP/HTTPS
		  * 389, 636: LDAP/LDAPS
		  * 88, 464: kerberos
		  * 53: bind
		UDP Ports:
		  * 88, 464: kerberos
		  * 53: bind
		  * 123: ntp

	2. You can now obtain a kerberos ticket using the command: 'kinit admin'
	   This ticket will allow you to use the IPA tools (e.g., ipa user-add)
	   and the web user interface.

Be sure to back up the CA certificate stored in /root/cacert.p12
This file is required to create replicas. The password for this
file is the Directory Manager password
:: [   PASS   ] :: Running 'ipa-server-install --setup-dns --forwarder=192.168.122.1 --hostname=rhel6-4.testrelm.com -r TESTRELM.COM -p Secret123 -P Secret123 -a Secret123 -U'
----------------------------------
Added host "bz817080.testrelm.com"
----------------------------------
  Host name: bz817080.testrelm.com
  Principal name: host/bz817080.testrelm.com
  Password: False
  Keytab: False
  Managed by: bz817080.testrelm.com
:: [   PASS   ] :: Running 'ipa host-add bz817080.testrelm.com --force'
:: [   PASS   ] :: Running 'mkdir /tmp/certdb'
:: [   PASS   ] :: Running 'echo Secret123 > /tmp/certdb/passwd1'
:: [   PASS   ] :: Running 'certutil -f /tmp/certdb/passwd1 -N -d /tmp/certdb'


Generating key.  This may take a few moments...

:: [   PASS   ] :: Running 'certutil -f /tmp/certdb/passwd1 -R -s 'cn=bz817080.testrelm.com,o=testrelm.com' -d /tmp/certdb -z /etc/group -a > /tmp/certdb/bz817080.csr'
:: [   PASS   ] :: Running 'ipa cert-request --add --principal bz817080/bz817080.testrelm.com /tmp/certdb/bz817080.csr > /tmp/certdb/bz817080.crt'
  Certificate: MIIDHDCCAgSgAwIBAgIBDDANBgkqhkiG9w0BAQsFADA3MRUwEwYDVQQKEwxURVNU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  Subject: CN=bz817080.testrelm.com,O=TESTRELM.COM
  Issuer: CN=Certificate Authority,O=TESTRELM.COM
  Not Before: Wed Jan 16 02:52:20 2013 UTC
  Not After: Sat Jan 17 02:52:20 2015 UTC
  Fingerprint (MD5): 92:6b:5a:e3:39:65:b3:ff:f2:f9:65:fa:e6:b3:68:8a
  Fingerprint (SHA1): c0:97:61:44:72:25:d0:63:f2:80:f7:4b:9f:92:42:fc:ea:38:80:67
  Serial number (hex): 0xC
  Serial number: 12
:: [   PASS   ] :: Running 'ipa cert-show --out=/tmp/certdb/bz817080.crt 12'
:: [   PASS   ] :: Running 'certutil -f /tmp/certdb/passwd1 -A -n bz817080 -d /tmp/certdb -t u,u,u -a < /tmp/certdb/bz817080.crt'
Request "20130116021422" modified.
:: [   PASS   ] :: Running 'ipa-getcert start-tracking -d /tmp/certdb -n bz817080'
:: [   PASS   ] :: Running 'certutil -f /tmp/certdb/passwd1 -A -n bz817080 -d /etc/httpd/alias -t u,u,u -a < /tmp/certdb/bz817080.crt'
Request "20130116021439" modified.
:: [   PASS   ] :: Running 'ipa-getcert start-tracking -d /etc/httpd/alias -n bz817080'
ipa         : ERROR    Some certificates may still be tracked by certmonger.
This will cause re-installation to fail.
Start the certmonger service and list the certificates being tracked
 # getcert list
These may be untracked by executing
 # getcert stop-tracking -i <request_id>
for each id in: 20130116021439
Shutting down all IPA services
Removing IPA client configuration
Unconfiguring ntpd
Unconfiguring CA directory server
Unconfiguring CA
Unconfiguring named
Unconfiguring web server
Unconfiguring krb5kdc
Unconfiguring kadmin
Unconfiguring directory server
Unconfiguring ipa_memcached
:: [   PASS   ] :: Running 'ipa-server-install --uninstall -U 2>&1|tee /tmp/ipaserverinstall_bz817080.out'
:: [   PASS   ] :: File '/tmp/ipaserverinstall_bz817080.out' should contain 'ipa.*ERROR.*Some certificates may still be tracked by certmonger.'
:: [   PASS   ] :: File '/tmp/ipaserverinstall_bz817080.out' should contain 'This will cause re-installation to fail.'
:: [   PASS   ] :: File '/tmp/ipaserverinstall_bz817080.out' should contain 'Start the certmonger service and list the certificates being tracked'
:: [   PASS   ] :: BZ 817080 not found

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

http://rhn.redhat.com/errata/RHSA-2013-0528.html

I appear to still be seeing this with ipa-server-3.0.0-26.el6_4.2.x86_64

Can you open a new bug with the details (what files, configuration, etc not restored) and reference this one?