I have both versions of the game and they are the same, except for text and voices. Anyway I noticed that too.
I guess, like other OST songs maybe longer or even slightly different. I know Chrono Trigger and Xenogears had longer versions to songs as well as unreleased tracks.
I haven't heard all the music from the OST so can't comment on all of it, but that song is quite different for sure. But there is a US compilation to the OST, are any different from the Japanese?
http://www.amazon.com/Selections-Final-Fantasy-Hitoshi-Sakimoto/dp/tracks/B000IU3YA0/ref=dp_tracks_all_1/103-0935292-5356648?ie=UTF8&qid=1176935649&sr=1-2#disc_1
Anyway to answer your question that song in game is the same in the Japanese version, it's just oddly very different on the CD...dunno why.