To add fuel to the fire, some GFWL achievements aren't being updated on my profile, even though I see the pop up in game. The Steam achievements go through fine. It's been surmised that save file losses has to do with the glitchy achievements. So, the best way to avoid the save glitch is, after unlocking an achievement, make sure you trigger another save, such as getting XP, entering another room, or picking up a trophy. Here's the ones that I was affected with so far:
1. Communication Breakdown
2. Serial Killer
3. Dial Z for Murder
4. Stop the Clock
5. AR Knight
6. Brainteaser
7. Sphinx' Riddle
The first 6 can be redone in New Game + (you actually have to do them again in order to unlock the 100% achievement). Sphinx' Riddle is 1 time only (collect all of Catwoman's Riddler trophies), so I would hold off on doing that until it's patched. I would hesitate to do the challenges too because they're one time only and I would hate to have to redo them all under a new save slot.
All in all, an awesome game. I'll hold off on doing anymore of the achievements until a patch fixes it. This is the only GFWL game that I've had issues with achievements and save files with.