I have some additional info that, hopefully, Telltale can use to pinpoint the problem with saves being overwritten and find a fix. Here's my story:
When I downloaded episode 4 today, I had two saved games: mine and my girlfriend's. The third slot was blank. My girlfriend and I had both finished episode 3, and so I selected my file (the first slot) to start playing. When I did, I realized the "previously on the Walking Dead" cinematic was showing scenes from her game. So, I quit out.
I then loaded up her game, out of curiosity. Instead of loading her file, the game started up a new game -- as though I selected the third, blank file. In so doing, the game overwrote her data, erasing her progress.
I then tried to start up MY game again. Big mistake. This time it started MY file from episode 1 as well -- probably because it loaded my girlfriend's now-reset file, starting me from scratch. So, here's what I think is happening.
I don't think the game is stuck on loading one file in particular -- I think the glitch has something to do with the game misinterpreting which file you mean to load. When I selected the first slot, it loaded the second slot -- my girlfriend's game. When I selected the second slot, it loaded the third -- the blank file. As further evidence -- normally when you select "Play" from the main menu, the next screen automatically highlights the first game file (slot 1). I noticed when this glitch was occurring, the SECOND save slot was automatically highlighted -- suggesting the game is stuck on pushing your normal selection down one slot. Pick slot 1, it loads slot 2. Pick slot 2, it loads slot 3.
Hopefully this helps. I'll answer any further questions as best I can.
Oh, and I've started replaying my file. I've deleted episode 4 and will only redownload once a definitive patch is released.