I'm having the same problem with a number of albums. 12 songs will match fine, but one track -- somewhere randomly in the middle of the album -- will upload instead. Out of 10,000 songs, I had around 2,600 uploads.
There must be some way to fix a song and then ask iTunes to retry the match for that song. Anyone?
I tried editing metadata and even resizing the song to be exactly the same length as the iTunes 'official' version. Many times on old rips, the songs would have an extra few seconds of nothing at the end. *shrug* Messing with these things did not help.
In order to ask iTunes Match to look at the files again, I renamed the original file so that I wouldn't lose it, and deleted the item from my iTunes library. There is a dialogue box that asks if you want to delete the item from iCloud. I selected this in order to clear everything out, everywhere. Then I added in the new version of the song that I'd resized, or alternately the newly edited metadata version. I appeared in the library with a status of 'waiting'. Once, it started updating iTunes match immediately. Another time I had to prompt iTunes match to update via the store drop down menu. In each case, all it did was re-upload.
I think we're looking at something perhaps incomplete in Apple's own data about their songs. Either the matching criteria for that song is incomplete or there is a conflict somewhere internally... perhaps the song is the 'same' version on two or more albums and iTunes match doesn't know what to do?
It's strange because there were things from years ago that I ripped from cd, clearly made a typo in the metadata... yet iTunes 'matched' these. Eh, maybe it will just take some time to get matching perfected.