Ohh, I believe this is because of extra files being included in the save data by accident. I'll make sure these aren't present going forward, but to fix it you can either delete everything under ...sixtyninedays\Saved\SaveGames, or if you have an old version of the game with you old save files, you can simply move them to the new version.
I'm not sure why 69 Days After saves the data in a different spot than my other games, but it's certainly something I plan to fix before the final release of the game.