Sounds to me like it might be a power supply issue. As a test, open a SNES ROM and start playing. When the slowdown occurs, is there a square rainbow icon in the top right corner of the screen fading in and out? If so then try a higher rated power supply and the issue will (probably) disappear.
I was pulling my hair out trying to get to the bottom of why all SNES roms and certain MAME ROMs (MK2 / UMK3 mainly) were suddenly running like crap, then I noticed the slowdown only occurred when the rainbow icon appeared. I had recently changed to a different power supply so I changed back to the old one again and performance suddenly became perfect! (And no rainbow icon!).
Hope this helps!