Just had similar problems with a cd I burned yesterday...
I didn't realise how stupid the inbuilt mp3 cd player really is
(stupid is a strong word) but it seems that it only reads the file names in "track listing" view (and even then only the first 10 characters or something) not the ID3 tags that are embedded into the songs. It does read the track information when playing the song though (why can't it just do this from the start?)
Haven't checked for the numbering of tracks although if I have to number all the tracks before burning them in that will be very annoying and you will lose information due to the aformentioned cap on track listing characters!
Not a very good solution if you ask me, my old Alpine CD player worked perfectly with mp3 tracks.
That said though what are the possibilities of Honda bringing out a firmware update for the in car system, fixing these issues (reading id3 tags to organise songs) and maybe improving it? How cool would it be to have album art aswell?