I don't think they are judging your settings in general, but for example in Yoshi you can not use frame skip (happens in any graphics plugin I tried ex Rice), since the game uses frame buffer effects to draw the back ground. And thus frame skipping makes the game unplayable as loveyy mentioned.
Hmm I'll try Yoshi without frameskip,i I was playing after I posted this and Yoshi Story froze on me and maybe it's because of the frameskip.
Anyway I've all noticed some bugs to report (no pictures or savestates because I'm not posting this on a computer, but my ipod)
Pokemon Stadium (U)
Some textures show up during attacks such as Blizzard and stay there
The icons for the Trainer and Pokemon still don't show up (kinda expected though)
When grabbing a Jiggy, banjo's shorts and mid chest turn black
The enemy's that wander Grunty's Lair have glitched colors
Grunty's eyes will glitch colors