Yeah dont worry about the "Set Auto Max Skip Frames to 1" to YES for now. It cuts the FPS down to like 30fps.. but like you said the animation is not as smooth, even if the game is more playable.
I'm gonna be upping a zip file with three versions of snes9xbox.. 1.51, 1.52, and 1.53. Do me a favor and try Contra III and FF VI in 1.52 (and 1.51 if you feel like it but 1.51 has the old sound engine). Let me know how 1.52 does compared to 1.53.
Once I'm done getting that up to the FTP I'm gonna send dante_ali those and the source for 1.53 (or anything else he happens to need).
Oh and I'll add Aladdin to my ever growing list of games to check..