I had similar, but not exactly same thing happen 3-4 years ago, but this is evidence that GA can tweak the list if he/she is in the mood...

I had made resi on the phone with 15,000 mile confirmed upgrade. I went online and printed my itin with seat assignment.

When I got to airport I was given BP with a seat in Y. I showed my printed itin to the GA who said they had downgraded me because the phone agent wasn't authorized to process that upgrade and it needed a supervisor to sign off on it. I showed the GA my printed itin with confirmed upgrade. A few keystrokes later she said "You are #1 on the upgrade list now". That may have been a way to get me to step aside, but 10 mins later, she calls my name and gives me new BP, so it all worked out in the end.