When using the autonumbering tool to renumber files that already have an existing track number, the option "Add a leading zero" works intermittently. Sometimes, the new track number has a leading zero, sometimes not.
The only workaround I found is to first erase the track number field of the selected files (i.e. set to blank), and then run the autonumbering on the files. In such a case the leading zero option is behaving properly.
This happens with WMA files; haven't tried with other types.