The direction of your guess is the only plausible explanation if the Pandora was indeed in proper Standby and not only in Low Power Mode BUT nevertheless the game has progressed as much as real time happened. Maybe some games calculate everything which happened in that long execution pause at once on resume, (and drop quite many many thousand frames to catch up).
Yeah I think that's exactly what's going on, it all depends on how the games are coded to react to large time jumps.
Super Geometry Dust: Sounds like a problem with SGX driver, I already know it can't suspend properly
while 3D is active, not much can be done here because it's a closed blob for the most part.
Standby test in various PND applications + dmesg: Not much [to say], except that most of things you tested fail to suspend properly, I'm
guessing it's related to sound, no ideas how to fix that at the moment.