Well, I sat down with the US version of ff7, reinstalled epsxe 1.01 so I could start a new game, and played with different settings and plugins tonight and managed to accomplish absolutely nothing. The timing is very consistent from test to test, just wrong. Bleh.
I'd have to guess it's a timing problem in the spu code in epsxe itself (either that or a problem in the code of every spu plugin, which I suppose is possible but not terribly likely). I figured it was a problem with the PAL/NTSC timing, but it doesn't seem to be; when autodetect is on, the game time is accurate but the music is too slow. If I set the fps limit in Pete's up to about 66, the music speeds up to about normal, but the clock runs fast. And regardless of what I do, the music just isn't syncing up to the movie.
Ah well, maybe they'll have this one nailed down in the next version.