trotter--
Since you're adapting all the names, is there some pressing reason why they can't be "01-Name Of Song.mp3" or
"(01) Name Of Song.mp3" or similar? Because I'm not seeing an identifiable separator otherwise, and I'm surprised you're getting even half your songs assigned correctly.
EDIT: I guess I'd better back up a bit (that's a fancy way of saying "oops"). Filenames aside, are you positive that the uncooperative tracks have proper track # tags? If yes, try doing a libray tools/update from tags on ONE file. If that helps, I would do that on all the naughty ones. And no, you shouldn't have to futz that much, but somebody smarter than me will have to explain why the problem is cripping up in the first place.
If not, this is why I name my files with bullet-proof separators, so the tags can be darned at will. I've made a high art out of fool-proofing, of necessity. With rich filenames I can get back a lot tag of the info that I periodically throw away.