Solved it yet?
I'm just a novice user, but I can give you my two penneth...
I've had this and similar issues. The solution, for me, was realising that what matters is the actual field name.
A program might show "Disc #", but when you enter in a disc number, it in fact writes to a tag called "discnumber". Then you load the music file into another software, and it looks for "discno" and finds nothing, and therefore displays nothing.
There are no universal standards for tags.
My FLAC tags were all tagged with "discnumber" in MP3Tag. However, MC tries to look for "Disc #" (I believe). Therefore, I had to convert all of my "discnumber" tags to "Disc #". The good news is, it's very easy to make such conversions, at least in MP3Tag. I press 'start', and within a matter of minutes, 10,000 or so files are re-tagged.
I have decided that MC will be my tag standard, as it is the only serious playback software I use. However, I find mass tagging within it rather cumbersome. My solution is to take a dummy music file: Fill in data for every single tag, within MC, plus add whatever custom tags you might use. Then, load the file in MP3Tag and select "show extended tags". You'll then see what the exact field names are, and you'll be able to batch tag very easily, in order to make your tags MC compatible.
Just remember, you'll have to tag different file types separately (in MP3Tag). Fields work a bit differently in WMA, MP3, and FLAC.
The beauty is, once everything is finally tagged, MC does an excellent job at managing the collection. I no longer have to think about fields and file types. Also, I can make small changes to tags, and MC is smart in that it knows which field to change in which file type.
Hope that helps.