I keep running into this issue where no matter what I am doing, if I exit the game and go to the main menu or just go to the main menu and exit to desktop, whenever I try to load back up any save, the game goes from full screen to windowed mode and drops the fps so low that it's essentially unplayable. On top of that, the cart spawns inside my shop and is "glitching" out by the wheels bouncing around wildly. I never run into this issue while playing, sleeping, or anything. The issue only occurs when I try to load up any and all save games. I've had to restart my playthroughs every time that I want to play.
The latter part of your post is why the first part has FPS drop - If you DM me the save file over on Discord, I can help you fix that part.
Someone, whether it is me or not, must absolutely fix one of your saves, or give you a non-afflicted save, For the few people that have the issue you have, it always happens no matter what when saving the initial time.
As for the windowed mode.
It boots in fullscreen by default, but the settings file it creates is a small resolution + windowed mode - have you not altered your in-game graphics settings...? Personally I recommend making it match your desktop resolution, and leaving it windowed
with a matching resolution, you won't even barely be able to tell its not fullscreen.