Disable steam cloud (thanks!).
Tried Sizemore's fix and it still didn't work. Deleted the TWD folder from Documents, started a new game from Ep2 since that was were my save was from. Played about 10 minutes to create some saves. Used the timestamp tool to change a save from near the end of Ep2 from the original playthrough to the timestamp of my latest save on the fix playthrough. Overwrote the fix playthrough save with the file from the original and restarted TWD. Game picked up with my save (near the end of Ep2) so I played the rest out. Ep2 finished, let the credits run. Went back to main menu. Click play and it went to Ep3 and once again asked me to randomly generate choices.
Now what the hell do I do?