Track Number Format, Padding with 0

AFAIK the mp4 tag format does not support leading zeros at all. So check what is wrong with the mp4 file.

Yes, this is always the case.
If you really want leading zeros, then, after you have assigned the correct ascending number, use an action of the type "Format value" for TRACK
Format string: $num(%track%,2)
this works only on files with the total number of tracks saved in TRACK.

See also here: