The track counter sometimes resets within the directory, leading to wrong numbering.
I ran the wizard on a large number of folders at once [settings: start with 1, all boxes checked] and I noticed the reset can be caused by a directory containing mp3s, either having different bitrates or having different tag types. Screenshot depicts the second case, it should be tracks 01-04 of 04 not two times tracks 01 and 02.
Unfortunately the exact outcome also seems to depend on how many files where selected and sometimes I can reproduce it and sometimes it works fine on a second run. Does anyone know more about this?