Under Interfaces -> LAN do you have Prevent Interface Removal checked? I saw what you're describing when testing failover. Shutting down the primary the VIP would move to the secondary as expected, and it would return to the primary when that host came back up. CARP status in the GUI looked correct in both states, but my ping check to the VIP started showing DUP messages as you describe. Unchecking the Prevent Interface Removal on the LAN interface solved it.
So wild guess that preventing removal is also preventing some kinds of reconfiguration.
So wild guess that preventing removal is also preventing some kinds of reconfiguration.
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