So, I've been looking further into the issues with saving- I haven't been able to replicate the bug, but that doesn't mean it isn't there. In the meantime, my recommendation, if you're running the game on windows, is to run the game in admin mode. I've done my best to eliminate anything within the game itself that could be interfering with saving- if the game bleeps and puts you back to the overworld, that means the save worked. I'll probably have to edit this to make the feedback on that work a little nicer.

If anyone has any other problems- or solutions to this one- please feel free to let me know!