So first I encountered the all too common "save games not showing up" issue. I fixed it and had all my progress from Episode 1 and 2. All good (no thanks to TellTale). Now I played around 2 hours of Episode 3 (so I've passed plenty of autosaves) and then I went to the main menu. When I tried to pick up where I left off all my Episode 3 progress was gone. Yay!
So anyone know how to fix this problem? I tried repeating what I did to get my Episode 1 and 2 progress to show but to no avail.