Ah! Okay, I think I know what the issue - the save system isn't fully supported in WebGL, (browser mode) which means most saving/loading while playing in browser might have similar bugs. I'll look into it and see if I can fix it, but it might simply be because of the platform. Luckily it should have no impact on the downloadable version, so at least the game isn't totally broken! I'd recommend playing on desktop if you can, or playing the whole thing in one sitting. I'll definitely let you know if I manage to fix the bug in the browser version, however!
Thanks a lot for reporting that bug, it's a huge help and I really appreciate it!!