We do nearly always add the pet in advance and then figure if we have to go to the counter for BPs then we'll just pay the fee there. As others seem to note, the payment process doesn't always go.smoothly at the front counter. So maybe we should do the payment in advance and see if that helps.
The last post about upgrades, that is what happened in BZN. Agent could not get things to work so unchecked in my wife, removed the pet and tried to re-add the pet and check her in again. In the 5 minutes she was trying to do that, my wife was upgraded to F for SEA-LAX and our guess is there were already the max number of pets in F and it would not let them add the pet back. My head was about to explode because I kept saying just move her back to Premium before her seat is gone. It was and so she got put in a middle Premium seat further back.