Yeah, It's odd, so I had the 'Add two leading zeros...' preset enabled, and if I try to manually change a double digit track, say 12, the preset will automatically change it to 012. I don't currently have any other presets enabled. This also occurs if I use the 'Auto-tag by Album' option, tracks 1-9 will properly have the leading zero added, but 10+ will have a 3rd digit added (010, 011, etc.)
Also I tried applying the manual search and replace filter to a list of tracks that already had double digit track numbers (01 to 13), the preview shows that it wouldn't make any changes to the track numbers, but when I applied it, all the tracks gained an additional leading zero (001, 002, 003, .... 013). Cheers.