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This bug is created as a clone of upstream ticket:
https://fedorahosted.org/freeipa/ticket/3668

This is because wrong trust flags are assigned to the intermediate CA certificate when importing the PKCS!#12 file:
{{{
$ certutil -L <dbdir>
Certificate Nickname                                         Trust Attributes
                                                             SSL,S/MIME,JAR/XPI

The Root CA                                                  CT,C,C
ca1/subca/server                                             u,u,u
ca1/subca                                                    ,,   
}}}

This in turn causes certutil to return an incomplete trust chain:
{{{
$ certutil -O -d <dbdir> -n ca1/subca/server
"ca1/subca/server" [CN=vm-131.idm.lab.bos.redhat.com,O=Subsidiary Example Organization]
}}}

Trust flags of intermediate CA certificates should be set to "c,c,c" to fix this.

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Filling Known Issue doc text for 7.0

Will this be fixed in the recent 7.3 fixes focused on CA-less to CA-full installation?

IIRC this has been fixed since 7.1.

Ah, closing as fixed then. Please reopen the bug if this happens again.