You are saying the PNR's are split because of the way the agent processed the payment when you decided to use a voucher for your ticket? How else could the agent have done it?
Good luck with getting compensation for your wife not getting an upgrade, I really don't see that happening. Maybe she will clear at the gate and the issue will be moot. I have the same issue as you, I am PLAT and wife is Gold. I have found it best to not pay in a way that separates PNR's. I have had to argue with Gate Agents who insist that our upgrade priority be split even when we are on the same PNR.