Cheers guys, it definitely looks like the problem Lonewolf describes. I tried it on an A500+ with a 68020 processor in WinUAE and it worked perfectly. Whether the LoadTrackerModule/StartTracker commands work with a 68000 is debatable I'd say.
I've played about with it a lot and still no joy. I even tried putting in some code to detect what processor is being used and if it's a 68000, use the standard LoadModule command (which isn't perfect) but still no dice.
I don't really see an easy way round this at the minute.