I don't know if telltale has a place to report bugs or anything, but I've found a way to reproduce the somewhat common duplicate prefs.prop issue (where a prefs.prop file appears in your walking dead steam folder, which mucks up all your saves until its deleted).
Whenever the walking dead game crashes, it creates this prefs.prop file. I've seen this happen every time the game crashes. I'm running windows 8 64-bit, steam and the walking dead are installed on a separate hdd. As soon as you delete the prefs.prop file that appeared in the walking dead steam directory the game reads my saves again.