I have the common issue with saved games. I didn't know about all these problems and started the game when my Internet connection was down at the ending of chapter 2. Now I have plenty of issues, sometimes I can't rewind chapter 2, choices are wrong, If I start the game and go back to the main menu the saved games change to a different version...
I already tried to move from TWD folder those .pref files to My Documents and viceversa but nothing it's working.
Here is the support tool file: http://www.sendspace.com/file/2hhywu
I already played chatper 1 and 2 on my friend's house on PS3 several months ago, now I played again in my computer after I bought the game... And now I'm not really in the mood of starting over again for the third time and I don't have too much free time.