Hey Andrew, I'd be interested to know if the problem shows up when you compile a module under emulation in SimCoupe?
I have a very similar problem to yours although for me it's not the tempo of the module that changes; instead one or two channels play their parts in completely the wrong key when compiled! The problem only occurs on the real hardware and because I develop on both I didn't notice the music was wrong for ages! I think this information from ellvis will clear things up though... thanks for that! I bet I have some wacky values sitting there as I had no idea what I was doing when writing my tracks :) Rob.