OK, I just tested the frameskip for GBA and SNES.
I tested the GBA with Golden Sun and found that it was exactly the same no matter which frameskip I chose.
For SNES, I tested with MegaMan X and Mario Kart. Frameskip worked perfectly for both. In the case of Mario Kart, using frameskip made it significantly faster.
What games were you using it on?