I had a similar problem. Not with all my compilations, but with one particular compilation. So far, that is.
After I set the compilation check box for every song in the compilation, I used the Store -> Update iTunes Match menu item, and some of the "Matched" songs wound up with their compilation check box unchecked again.
I got around it by entering the same made-up name for Album Artist (say, "Compilation #1 Artists") for every song in the compilation. That kept all the songs together in iTunes.
But I'd hate to have to do that with every compilation I have ...
After I reported the above, I found that my workaround didn't really do everything I wanted. In iTunes on the originating Mac, the compilation looked all right. But in the Music app on my iPad, it showed up as two separate "albums." One had the majority of tracks in the compilation, while the other had 4 tracks that iTunes Match had arbitrarily turned off the compilation check box for.
I decided to start over. This project represents a compilation of 21 tracks that I am importing from a homemade CD that a friend sent me as a Christmas present. My friend took tracks from her own playlist of gospel favorites and made the CD for me.
I imported the tracks into iTunes from the CD in a way that I was using the actual track names and artist names, by the way, which means iTunes Match could be expected to match a great many of them.
That's exactly what happened. In iTunes Match, 5 of the 21 tracks were getting Uploaded, while the rest were shown as successfully Matched. But it was 4 of those 16 Matched tracks that were having their compilation check box arbitrarily cleared after the iTunes Match update.
I deleted the originally imported tracks, deleting them from iTunes itself
and from iTunes Match, and also putting the original files in the Trash. Just to see if it would help, I changed my iTunes import settings to use the AAC encoder, not MP3. Unlike during the first import, when I set up to do the import from CD that second time, in iTunes Get Info I checked the "Part of a Compilation" check box globally for all tracks
before I did the import. Then I did the second import.
When it was done, the iTunes Match update process was initiated automatically by iTunes, and at the end of it, all of my tracks
still had the compilation check box checked! This was in contrast to the first time I did the import, when the iTunes Match update process had unchecked the compilation check box for 4 tracks, as I said earlier.
I then (since I like to see album art of some sort for all my music) added some generic gospel album art globally to all the imported tracks in iTunes and manually re-initiated the Store menu item "Update iTunes Match." After the iTunes Match process had been completed that
second time for the second import, all of my tracks
still had the compilation check box checked! In other words, the entire "album" made up of the tracks of the imported compilation continued to be seen by iTunes as a single album. This time I did not even have to supply a phony Album Artist to each of the tracks of the compilation to get that to happen.
Better yet, the compilation "album" is now seen by the Music app on my iPad as a single entity, with the desired album art, and is not split up arbitrarily into two separate "albums."
I made two basic changes for the second import: (1) using the AAC encoder, not MP3; (2) checking "Part of a Compilation" for the to-be-imported tracks on the CD before the import, rather than doing so for the already imported tracks in the iTunes library after the import. I don't know for sure which of the two (or possibly both) made the difference.
