Yeah I had that enabled. What seemed to cause the issue was that i also enabled the option of custom upscaling filters for DSi on the startup menu, because it sounded like i needed that enabled too. Disabling it seems to have fixed the problem.
Don't know why, but everytime i try to apply some upscaling patches it just refuses to work. I've been trying for days now, but it doesn't want to change the upscaling method. Is TWPatcher working on the latest luma version?