MediaMonkey doesn't change the Track #'s. Maybe what happened is that they were taking from the filename when the files were scanned (you can disable Infer File Properties under Tools > Options > Library (this will auto-guess empty tags on scanning)).

Tools > Extensions > Auto-Increment Track #s can be helpful.

I have been doing a massive updating of my music over the past few weeks. Previously, before I added everything to MMW all tracks were number 1 - whatever the album finished on. Now, however I am finding that some tracks in hte albums are in the hundreds or thousands. Why is this? And, if I chnage them back will MMW go behind my back and alter them again?
Or is there a way to keep them set as I want, not what MMW wants?