Thanks for the suggestions SamIAm. I'm glad I'm not the only one. Well not
glad exactly, but it's comforting.
MEFX is certainly an option, but it glitches on the non-FMV cut scenes, while Mednafen plays those fine but the video/audio is glitchy. (Game is Megami Tengoki II BTW) Maybe I play it twice and edit the footage together?
(kidding) What is frustrating for me is that I already have a Hauppauge HD capture device that is awesome for most things but won't capture from FX at all.
It's interesting there doesn't seem to be a frame limiting feature to Mednafen, I don't know if it would help but I wasn't able to find one to try. I did try playing with the CD-ROM speed, video driver, and vsync but those did not seem to help in any combination I could find.
Not sure if I have a good way of frame grabbing from FX hardware while capturing audio separately but I'll keep that in mind. Wow, I actually just had a creepy thought. I could probably crack out my VHS deck and try recording to that and then capturing from it.
I might still have an older capture device kicking around too. Maybe I'll give that a try.