Using Garrett's advice from the comments, coupled with the answer to another question here on SuperUser, I managed to find two songs that weren't in MP3 format like the rest of my collection (it actually appears that I converted them from M4A in iTunes, but never deleted the M4A version of the file).
Using the question I linked to, I built this command line search string:
dir /s /b /a-d | findstr /v /r ".*\.mp3" | findstr /v /r ".*\.jpg" | findstr /v /r ".*\.ini" | findstr /v /r ".*\.itc2" | findstr /v /r ".*\.xml" | findstr /v /r ".*\.MP3" | findstr /v /r ".*\.itdb" | findstr /v /r ".*\.plist" | findstr /v /r ".*\.itl"
Most of these are iTunes related database and metadata files, along with MP3 (which is what my collection is in). If you have other media types supported by Google Music, you might have to edit this search to also eliminate those from the results.
Anyway, When I ran this, three files came up. Two were M4As and one was in iTunes/sentinel (I'm guessing it's an extensionless iTunes file of some kind). I eliminated the M4As and all was well with the world.