In playing around, that seems like it is the issue. Files that are normally giving problems work properly after I go in and re-save the numbers in Tag Studio (making sure to re-save the info to the files).

The files now show up as 1, 2, 3.. 8, 9, 10 instead of 01, 02, 03.. 08, 09, 10. The 8 and 9 tracks are in the right order, whereas with the leading zeros, the 8th and 9th tracks had no track listings in their properties.