Save issues are often difficult to resolve.
Please start with verifying your game cache files
Then disable steam cloud again.
It's possible that your issue is caused by having multiple prefs.prop files, which sometimes happens for unknown reasons.
There should be only one prefs.prop, and that's in the savegame folder:
Win Vista/7: %USERPROFILE%\Documents\Telltale Games\The Walking Dead
XP: %userprofile%\My Documents\Telltale Games\The Walking Dead\
Please check if there are additional prefs.prop files in the install folder
(e.g. \Steam\SteamApps\common\the walking dead)
or its subfolders.
If so, make a backup copy of the prefs.prop and delete it from the install folder.
If that doesn't help, make a backup copy of the savegame folder's prefs.prop, and then try copying the install folder prefs.prop to the savegame folder.