ShaddyGames can you offer any advice on this? The variables are defined properly, so I'm thinking it's and issue with his save?
Looks to me like you save got corrupted, best thing to do would be to start a new save. Then just use the mod to skip through all of season 1, and then do the same to get back to where you are on season 2. That's the best advice I can give you, because this is not a bug in the game, I just double check it myself. You're also the only person who's reported this. I would NOT suggest ignoring it, or you will have problems down the line.
Unfortunately as I said, I think your save got corrupted. Which can happen on any renpy game, I've had it happen to me more than once. Is it the norm, no, but it can happen.