The soundtrack version is incomplete, so it's missing the loop point. Not sure about the extended version. Did you check it?
Haven't listened it for a while, gotta check it today, especially now that new Winamp has gapless mp3-playback which should be little bit with the looping. Also the soundtrack version of Battle Train is missing the best part of the track anyways, which sucks, so probably the extended version is better one to be looped.
Still, Konami seems to like screw me again. First no Suikoden III in Europe and no Neo Contra ost, and now it's damn hard to make PSF2 rips of both PS2 Contras. What next Konami?
Edit: haha, no need to even edit the soundtrack version, been looping it for few hours at work now.