I feel for you. I had no end of trouble with disks 1 and 2 of my "Greatest Hits" copy of FFVIII, fresh out of the wrapping. My PS, which I dug out of the closet, kept "coughing" and "choking" through the course of both disks, though it played disks 3 and 4, and all of FFIX just fine.

You might try opening the disk casing/cover/housing thingy on your PS/PS2 when the FMV comes up. I have *heard* that you can skip FMVs that way, but I know of no way to actually "deactivate" them.