Do you have trouble with any other DOSBox games? I wouldn't think it is related to your controller, but you can simply unplug/disconnect it to test. You can try switching to a different output method.

Honestly the first time this happened, the most recent play of another game in dosbox had zero problems, and that was toonstruck.
Never before had to change any configs for a game that runs in a dosbox from here so I am kind of out of my depth with looking into changing things up.

Couldn't even figure out how to set it to window mode to check if its simply having trouble with my native screen resoultion. Doesn't help that I barely got time to look into it because of work and other obligations.
Pretty much the reasson why I ended up posting here, since I really want to get this working.

Gonna try fiddling with the controller later and hope it helps without having to kill the game via taskmanager again.

Toonstruck actually uses ScummVM not DOSBox.

If you look in the game's directory or Start menu folder, there should be a shortcut for a setup/config program where you can select a different output mode and turn fullscreen off.

You can also use Alt+Enter to toggle between fullscreen and windowed when DOSBox is running.

By now I got it to work.
I start it in full screen and still have the green and purple display problem, then switch to windowed.
Strangely that works and I even got my joypad set up to be useable as well.
Still no clue why it does not start with correct display from the get go.