I finally figured it out! It's the disk # tag, I deleted it all with mmw, and that fixed it. You don't need a disk # for a single disk release anyway.

Check Disc# besides making sure Track# is in order.

I know this is an older post, but I have the same issue, and it's driving me nuts! I have tried stripping out the tag data and replacing it (versions 1 and 2, with mmw), renaming the files, I have deleted them with mma, and replaced them, and just about every combination therof. Occasionally it works, but I am still stuck with these "100x" track numbers, and I have no idea where mma could be getting them from.

Check the Disc# of those files. If they have no value, were the files Synced by MMW?

As seen in the screenshot, alot of my tracks get numbers added infornt of them, messing up the order.
Track 10 is actually track 10, but 1001 should be 1 an so on. I tried changing the numbers by editing the song info in the app but that doesn't help.
Any ideas how to fix this?