The simplest solution: Set the movement controls to the Dpad, not the analog stick. Seriously, so long as the controller's plugged in and you set up the controls for it, you don't need to do anything else.
Whenever I use miniusf files as stage music, it ends up sounding all stuttery, and I mean REAL stuttery. I've installed the plugins properly, I've included the USF file in the same folder as the miniusf, but no matter what, it just won't play right. It's not like my computer sucks at playing those back, it all works just fine on Winamp, but it just doesn't work in MUGEN. Any help?