I've been playing through TWD without issue until I reached episode 4. I played up to the school then quit the way I normally did and came back the next day. My save data from that period was gone, I was back to the end "cut-scene" of Episode 3. It showed in the load game data that my only saves were from a few days previous, too. When I tried to load it I got the message about losing all data to my last autosave.
So I restarted from there, played through about an hour and exited again. Same thing happened.
Actually, I'm over-simplifying a bit, each time when I said "Yeah, rewind anyway" the screen would go black and nothing would ever happen, I'd need to uninstall the whole game and re-install, then I'd be able to load my "old" data.
I tried copying the prefs.prop file from my save data folder to my steam folder as described here: http://forums.steampowered.com/forums/showthread.php?t=2913992 with no joy. Thing is, if I look in my save data folder, I see new save games from even last night, so I'm confident it's actually saving my progress, it just never shows up in the load menu again.
I saw a note in the forum about disabling cloud sync, so I did that in Steam as well and started replaying from the end of Episode 3 and still the same result.
I like Episode 4 and all, but I'm really tired of playing the same hour-ish of it over again trying to make the same decisions each time.