Thanks for letting me know :). I think I found the first bug, it has to do with the towns chest having a different size. I suspect it happens after getting chest expansions . I'll look into the incorrect stairs as well.
I've uploaded a new version which fixes the problems. You can copy the save and state folders to the new version to not lose save data. Thanks for reporting the bugs, I hope I managed to solve them, please let me know if you run into any problems. I did a small art update as well.