yea i get a similar problem. it's a problem with how it pulls the image from the metadata. iTunes can pull it right from the meta, or through a url, or a link to a file on your hard drive. android pulls it only from the meta (like windows media player). actually i bet if you checked out your library in wmp pretty much all the same songs would be missing artwork.
unfortunately for me, i got bored and made a project out of getting all my album art back before iTunes got into the cover flow thing, so a lot of my stuff is calling from a file or a url, which means it's blank on my droid.
which is driving me ****ing nuts. I get really anal about my music organization and it's like nails on chalkboard to me.
one way to resolve this (the long way as far as i can tell), locate the albums that don't have art on your phone. find them in your itunes, go to the info, delete the album art in there and tell iTunes to download the artwork. this will store it in meta for the file. then just copy them back over and overwrite the old files, they should have the art now. the only problems with this are if you're like me and have a few albums that iTunes can't find the art for, and you get fed up easy.
i really hope someone else has something better to suggest because i've already given up on this.
i really wish the stock player had a built in tool for this because it seriously does drive me crazy.
oh i guess i should mention that i've never used tunesync, i just do it all manually.