Ok, the Final version is the one that is current. Are you using Wine on Linux, since I noticed that the configuration manager refusing to work is a issue with Wine, but it works fine with Steams Proton. I would also try recomending using the X86 version as well and see if there is any difrences. Proto 1 is the first version of the game were I was just messing around to see if I could get the player moving at all for the record, and Proto 2 is when I get a background with a intractable key and door, however, the room doesn't transition over. I also noticed that you didn't give Proto 2 a try either, but I'm not going to force you to.
I'm currently overhauling the game to have a bit more of a solid base a more defined configuration manager that doesn't just get skipped in Wine, audio support, puzzles to solve, and more. Right now all I got was the version that I made (but didn't upload) for GMTK up right now, and the reason why I didn't upload it was because I ended up stuck on a bug where a table would not spawn in the next room over.
So yes, some of the issues are allready known issues with the game. I don't know what caused them besides a error of the underlying code, and that is what I'm currently working on to provide a more stable experience.