Hmm... Framiga brings up a good point.
If the tempo is wrong in a MOD, the samples won't break/loop at the right point, and they will pop and click.
Also, as odd as it sounds, PAL/NTSC screenmodes can affect playback.
You may want to try another MOD player. I've found that DeliTracker is probably the best at detecting what type of mod you are trying to play, and then figuring out how to best play it back on your system. (Or at least it works darn well on my 4000/060 OS3.9BB2 system)