Check the settings in the emulator. If the NTSC filter option isn't disabled, disable it.
HOLY CRAP!!!!!!!!! It works now. Like the Dev says, it is slow, but runnable. CIA has Sound (dont know if the .3ds or .3dsx do or not). Graphics are perfect. Wonder if it would be possible, if you have the Display at 1:1, to have a Background layout like BlargSnes does. Could have a Image of a old TV Set so it looks like you are playing it on the TV. LOL.
Excellent work Dev. VERY Excellent work. SMB runs great despite the slowness of it, but if it takes time, it is all good.
Edit: Note- Games tested all have the Stuttering issues. As of now, like the Dev says, it is a WIP. Can not be helped. CIA has Sound.
Super Mario Brothers: Looks great. some very minor graphic issues, but otherwise near perfect.
Super Mario World: Graphic problems. Seems to run a little slower than normal.
Super Mario Brothers 3: Graphic Issues. Game kind of has performance issues when you hit a "?" Block. Otherwise, no problem.
-Also, if you use GGGuy Program to add Cheats to the ROM Image, it will work on the Games. However, this Game, when starting out, Mario is rather messed up Graphic wise. But once you grab a Powerup, you are good to go.