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Description of problem:
ssh(1) seems to try only the first nameserver in /etc/resolv.conf:
localhost:~> rpm -V openssh-clients
localhost:~> host target.example.com
target.example.com has address 192.168.1.1
localhost:~> ssh -vvv target.example.com
OpenSSH_5.3p1, OpenSSL 1.0.0-fips 29 Mar 2010
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: Applying options for *
debug2: ssh_connect: needpriv 0
ssh: Could not resolve hostname target.example.com: Name or service not known
localhost:~> cat /etc/resolv.conf
nameserver 192.168.168.254
nameserver 192.168.1.254
localhost:~> sudo vi /etc/resolv.conf
localhost:~> cat /etc/resolv.conf
nameserver 192.168.1.254
nameserver 192.168.168.254
localhost:~> host target.example.com
target.example.com has address 192.168.1.1
localhost:~> ssh -vvv target.example.com
OpenSSH_5.3p1, OpenSSL 1.0.0-fips 29 Mar 2010
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: Applying options for *
debug2: ssh_connect: needpriv 0
debug1: Connecting to target.example.com [192.168.1.1] port 22.
...
Version-Release number of selected component (if applicable):
openssh-clients-5.3p1-52.el6_1.2.x86_64
cannot reproduce with "dead" 1.st nameserver. There may be problem when 1.st nameserver responds that host do not exist. But this is resolver issue.
Can you verify (by tcpdump, wireshark or some similar tool) the DNS responses please.
Yes, in my testing the first nameserver was not dead but the target system was unknown to it (the second nameserver had been set up for a test network while the first one was an organization wide nameserver).