Strange...ICQ me for the real file I had to convert to xm to get it to work with my level.

AFAIK the music engine used in JJ2 has very limited Impulse Tracker (.IT) support. Several effects are missing and there's no proper support for instruments.
Furthermore when you're using a program such as ModPlug Tracker to make your .IT you must remember that .IT-files written in ModPlug may contain some non-standard features.

I'll probably post a detailed doc on this one of these days.