Core Issue
In the Cisco CallManager 4.x cluster, when a new phone is registered, it is registered to the Subscriber server not to the Publisher server. There are no effects on the functionality of the phones.
Resolution
The registration of the IP Phones depends on the order in which the Cisco CallManagers are listed in the Cisco CallManager Admin page > System > Cisco CallManager Group. IP Phones are registered to the Cisco CallManager highest in the group. Also, for phones to failover, there needs to be IP Address in the System > Servers or else DNS needs to be configured.
Refer to Cisco Technical Support IP Phone FAQ for more information about the IP Phones registration and other FAQ.