So it's a player problem?
You have to find out what the difference is between the files that show up properly and the others that don't.
I suspect that the player behaves like most others and simply ignores data in the field DISCNUMBER.
I also suspect that you have minute differences in the field ALBUM for the other files that show properly, like e.g. the discnumber also in ALBUM...
You have to check.
Just for inspiration: here is a thread that deals with ignored discnumbers and possible ways out: