Yep I have had nothing but problems on my playthrough so far.
Finished episode 1 fine.
Started episode 2 and all the choices in my game were wrong...
So I found a .prefs fix on the forums and it seemed to fix it ok.
Started episode 3, and my save game reported I was only at episode 1... so I just went to episode select and chose episode 3. All my choices seemed to carry over ok, though some things seemed odd here and there.
Also at the end of this playthrough instead of listing the choices that were made by the players of the game it simply listed choice 1, 2, 3, 4, 5 as the text, so I had no idea what each of the choices actually were....
Loaded it up to play episode 4 the other day, and yep same problem, game lists my save file as being in Episode 1.
It's sucking a lot of the enjoyment out of the game for me, but I'll forge ahead and finish the last two episodes in the coming days just to experience it. Most of the choices don't seem to even matter in the end anyways. (From my 1-3 playthrough experience)