I'll look into this when I have the opportunity, but could you copy/paste:
1. The original LoadBGM command.
2. If you're using it, the original PlayBGM command; otherwise, tell me how the track is being triggered the first time.
3. The PlayBGM command the second time, or how the updated loop settings are being triggered.
There's a possibility the system is attempting to play the system battle theme, which could interfere, but I don't have enough information to determine that. (And that wouldn't explain the problems with the pre-battle loop.)
Also, wouldn't hurt to tell me the length, in samples, of the OGG track and what its default loopstart and looplength are.