Here's my story:
I had the save game issue back when Episode 5 came out. I tried numerous fixes and nothing worked. Eventually I decided I would just replay the entire game during my vacation (which I am on right now).
Today I finished Episode 3. I closed the game and wanted to go back and verify that my save game still existed. Apparently this game syncs to the STEAM cloud (something I've never seen it do). I must have launched the game too fast and received an error. Now I've seen this error before and it's never given me an issue. It basically is saying it hasn't finished syncing. I've canceled this error and been fine in other games. This time when I loaded up the game all my progress from today is gone. It only shows my having played to Episode 1.
My save files exist in the My Documents folder. The prefs.prop file only exists in the My Documents folder. I've deleted any ones I've found in other directories. I've tried to turn cloud sync on and off for this game.
It's incredibly insulting that I have to worry that a video game in 2012 will not read my save file. It's the most basic feature in a video game and something all of them MUST get right. Worse yet, we've received pitiful support from Telltale. No information on a fix, no information on why this is happening. Nothing. Just a number of workarounds that other users have discovered.
This game was once in the running for my GOTY but not anymore. Going forward I will no longer be purchasing anything from this company and I'll warn everyone I speak with how pathetic the QA and Customer Support has been. You have no one else to blame but yourselves.