This is because the standard MP4 tag atom (trkn) can't store leading zeros. Till now, I wanted to save the information losslessy and created a freeform atom named "track" for tracknumbers with leading zeros. Since iTunes (and probably other software too) has problems with that, I've changed this with the current Development Build Mp3tag 2.43c and remove leading when saving MP4 tags.
Thanks for bringing this to my attention.
Best regards,
~ Florian