Had this issue happen to me today. No CPU flags on reservation after adding in cabin pet. Also not added to the upgrade list automatically after checking in with a representative. Went to a club agent to add me to the list manually, but it was giving her trouble given the pet, and while she was working on a work around, gate upgrades processed and I missed the potential CPU.

The club agent said there are no upgrades in advance with pets on the PNR now. And adding at the airport is a challenge as the system tries to block adding the passenger to the upgrade list... she said the help desk would take care of it, but in my situation it was too late.

Going forward I'll add the pet at the last minute after CPU clears? But that's a risk if there is no space left. Guess I'll just have to get used to sitting in the back with an in cabin pet or buy F.