Ok, here's what I noticed so far.
Steam Achievements aren't being unlocked.
Jack doesn't gain stat boost points after winning a battle.
The internal clock of the game is messed up somehow. I have 4 hours on Steam yet 6 hours on a save, I haven't opened the game through its .exe, only through Steam.
Scenes with characters I don't have in my party are still popping up. They are scenes I've already viewed before so that may be intentional, just threw me off.
Great game, still busting fat nuts as I go through it.