Itunes not tagging to actual file (esp. genre)

I just went through all 23,000+ tracks of my music and Labeled them with a genre system to my liking. Most of the files stick, however just over 1,900 of them don't. By stick I mean they're not being written to the actual id3 tag of the file for some reason and don't show up in other media players. (selecting convert to id3 tag has not helped). Below is a screenshot showing what I mean...
The track highlighted in iTunes has Genre labeled as Punk Rock, and no Genre listed in windows. If I pull the file up in mediamonkey or another player, the Genre will be empty. Is there any way to make the tags stick to the file? Does anyone know why some of them aren't? I don't see any rhyme or reason to when it happens. I'm sure they all have something in common, but I don't know what.

If you embed artwork to all files in an album it takes up more drive space.  It may not sound like much but if it is high resolution artwork and you have thousands of files it could represent a few GBs of drive space.  iTunes keeps only a single copy of artwork per album but this is only in iTunes library, not the files.
So if you really do want to embed artwork:
Script for embedding artwork - http://dougscripts.com/itunes/scripts/ss.php?sp=embedart

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