Hey thanks so much for the feedback, and for going through the effort of of bug reporting!
That first screenshot looks like the fullscreen option? When you change options there, the game saves a permanent variable. The game also saves other permanent variables depending on stuff you're doing, so I'm guessing this is the problem. I have one trick in the works to solve this, it'll be in this weekend's update so hopefully that works. We'll see.
I've just set up a discord actually if you'd prefer to use that: https://discord.gg/JKk6TbbUQu
Alternatively, I might swap the comments section on the itch page for a categorized discussion board, with a section for bug reports.