I had this very same problem and diagnosed it as a glitch with iTunes. You're not doing anything wrong. After much trial and error I have resolved an extremely simple and non file-altering fix. What I did firstly is instead of selecting "Entire Music Library", under sync music on your device's tab on iTunes I chose "Selected playlists, artists, albums, and genres". I then went in and selected all of my music by hand (yes, your hand will be sore after this, but you need to do this). I then realized that when I sync everything but the playlists my music library syncs fine. That means iTunes has a problem with playlists. I then noticed that for each album I was having trouble with there was a playlist with that title! To sum it up, If you sync up a playlist with the same title as an album it will confuse iTunes. Unfortunately, this means you may only be able to use playlists that are built into iTunes (the ones with the gear icons). select only those under the genre section along with everything in all other sections and your device should be complete.
TO SUM IT UP IF YOU DON'T WANT TO MARVEL AT MY CLEVERNESS:
1. Select "Selected playlists, artists, albums, and genres" instead of "Entire Music Library" on your device's music tab in iTunes.
2. Select Every artist, album, genre, and playlist except the playlists not marked with a gear.
3. Press apply and your device should have all of it's music.
Hope I helped!