I had a closer look, and I think I came across something.
I'll start with a picture of the album where I noticed I was missing files:
http://imgur.com/gq2Bu.jpg
The songs that would not reverse sync don't have file sizes listed. (1)
The track titles are incredibly long (2)
Going by this, I looked referenced another item that had a ridiculously long title, and surely it was missing as well. To double check, I connected the zune again and checked device> music, and again I can't see the file size.
http://imgur.com/1v2R0.jpg
I think, I can with some certainty say the Zune software is not handling long file names correctly.
I also took some time to go through each individual album, apparently I was wrong when I said the library resetter fixed the meta data issue. I've noticed a few albums are now missing track number order and a few stray missing album arts here and there- but that isn't too big of a deal. Is there anyway to get the developer's attention about this issue?