I've been getting the same issues on my Mac!
We are investigating this issue now but have not yet been able to reproduce it under normal play. Please keep in mind that if you use the Rewind feature on your current save game, you will need to play through Episode 1 on that save to completion before the choices will transfer into Episode 2. This is why we recommend copying your save to a separate slot before using Rewind.
If you’re currently experiencing this issue, please open the folder that you installed The Walking Dead to. If you find a prefs.prop file in this folder, move (move; don't copy) it to your save game folder and overwrite the file that’s currently there. By default, that folder is located here:
C:\Documents and Settings\USERNAME\My Documents\Telltale Games\The Walking Dead
C:\Users\USERNAME\Documents\Telltale Games\The Walking Dead