did you resolve your issue? I have same problem. all worked many years. nothing changed. but last weeks when connect office vpn and after some time dns stop working. but nslookup - work. similar your issue. 

Nexus 3000 is compatible with 100 Mb copper. http://www.cisco.com/c/en/us/td/docs/interfaces_modules/transceiver_modules/compatibility/matrix/100MB_Tx_Matrix.html#_Toc473122793 N3K-C3548P-10G GLC-GE-100FXSFP-GE-T (100M) 6.0(2)A3(1)

Do it on secondary (from cli restart Cluster View, restart "Cisco Desktop Call/Chat Service", "Cisco Desktop License & Resource Manager Service", "Cisco Desktop LDAP Monitor Service", "Restart Cisco Desktop VoIP Monitor Service") Then on primary. And...

Thanks Kim! Did You run CLI command (restart CCX Cluster View daemon) and restart services on both servers? Subscriber first and then Publisher?