I'm glad you noted that a FMV is supposed to play. I think that may be related. I did a pretty feature-light mod setup specifically because I thought it would minimize the chance of something like this happening, and I chose 'no change' for the FMV sequences. On my playthrough the FMVs haven't been playing at all. I've just been watching them on youtube. Other stuff I used includes all the PRP classic avatars, bootlegged models, team avalanche textures, PNG battles, and Scene Redux - better steal. (I have no idea what this really does, but stealing has annoyed me enough in past ff games that I decided I'd take a boost.)
I'm guessing the next step here is going to be reinstalling with a different FMV option but I'll wait for the 2nd opinion.