I THINK I figured out how to get all of my songs over! I have spent hours trying to figure this out and even went to the Genius Bar, and they had less of a clue that us here! Bottom line, when I tell it to Sync all music from the Music tab, it flips out when played on the phone. Even better, it shows that it will load all of the songs when syncing but when it's done, the blue music bar flips back to less songs and when played on the phone, they freak out again.
I thought it had to do with songs from cd verses songs from iTunes...nope didn't matter.
So....
For me, it definitely has to do with how you have the sync set in the Summary tab verses the Music tab. Right now on my system, if i select "Manually manage music and videos" on the Summary tab, it deselects the ability to select songs on the Music tab. (seems counter-intuitive but okay). When you select "Sync only checked songs and videos" on the Summary tab, then you can manually select the playlists and songs on the Music tab.
So that being understood, make sure Automatically Sync when attached and over wi-fi is OFF, attach phone. Select "Sync only checked songs and videos" on the Summary tab, select the playlists you want from the Music tab, then switch it to"Manually manage" on the Summary tab and force the sync. It worked this morning!
But what about the hundreds/thousands of songs not in playlists? Hmm, other than checking every artist, I checked every genre instead. I switched to "Sync only checked songs", selected playlists and all genres, switched back to "manually manage" and forced the sync. Voila! I officially have all 3300 songs on the phone and as of now, no flipping out!!