This could be pure superstition on my part (I'm not a programmer and based on my programming knowledge this seems like a weird interaction issue) but I think it might be a problem with room transition effects. I just made a test game and did some trial and error and I was able to replicate the issue with transition effects, but I wasn't able to replicate it with no transition effects. Something to try, anyway?
(also I started your game and am loving it; I'm gonna go finish now!)