the Metadata Pane does not save track numbers with 00 or 0 inside MP3 and FLAC. And the column “Track number” is empty, but not in other tools like foobar2000, Mp3tag and PerfectTUNES.
Hmm, that's not the case here with my MP3s. I did a few tests, file name contains 00, also the track number, but i can change and save whatever i want. Did you use any special MP3 tool prior to that?
My test was to rename an MP3 containing 00, also to set a track number starting with 00, plus a few random changes inside the meta panel. All changes were preserved so far. I also tested with the language changed to english, just in case that would have been a factor.