So, I didn't know it made extra files not included by the game. I deleted the files in 3ds and it worked. Sorry.
Found the issue while messing with settings. It's something to do with "3D anaglyph" being on.
The onscreen keyboard and numpad won't show up sometimes. It randomly shows back up sometime later.
If it is a setting, I can't find it.
Could y'all help me with this?