I'm not sure this was "clearly" a case of GA substitution. There are many other possible scenarios.

Also, remember, the OP was not on his original flight and was standing by for this flight, so it is likely that this contributed to either the OP being superceded on the upgrade list on the new flight, or that this simply added to the confusion

I'm not saying there weren't shenanigans, but I don't think it is clear at all from the information provided so far.