I am using the MC12 beta and the compilation tag works fine. However, I use Tag & Rename to set that tag, I don't think that there is an option in MC to set it. However, if the tag is set right, when MC syncs the files to the ipod, the compilation feature works as expected.
I have no problems with compilations in MC. They work exactly as I expect, and exactly the same way they would be if it was managed by iTunes. But I still cannot see the compilation tag in MC. I do not clearly understand how you are managing the tag.
Based on my understanding, MC mimics the behavior of iTunes. At the iPod level, everything is the same, but it is not using the iTunes compilation tag. The driver tag in MC is the Mix Album tag. The Mix Album Tag is a read only tag managed by MC. MC sets this tag based on the following condition; you have all of your tracks for an album in a single folder, and you have multiple artists for the tracks on that album. In this situation, MC sets the Mix Album tag and considers it a compilation and will update the iPod database correctly when you do a sync.
When you manage your library in iTunes (which of course no one really wants to do), there is a tag to indicate if the tracks on an album are part of a compilation. This tag is not the Mix Album tag that MC uses.
If everything is set up correctly in MC, the iPod will understand the compilations, but when iTunes looks at the same tracks, the compilation tag may not be set. So if you sync from MC, the compilations work correctly. When you sync from iTunes, the compilations are not treated correctly. You can set the tag in iTunes, but then you are managing the tags in 2 places.
So if you have compilations working correctly in iTunes. The compilation tag has been set in iTunes (either automatically or my manually updating the tag). If you have compilations working correctly with MC, it is because MC automatically detected that these tracks are part of a compilation. Not because the compilation tag was set in iTunes.