iTunes Music won't sync to my iPhone!

I updated iTunes about a week ago. Before that everything was normal. After the update, I tried to sync some new music onto my phone and only a few specific songs synced, with the others being "greyed out" and with the red circle red square (stop sign) beside them. The music that did sync was not purchased from the iTunes store. I took it into the Apple store and they did a factory restore, but it didn't help, and only purchased music would sync. The person helping said that music not bought from the iTunes store is not programmed to sync, and never would...but it did before the update with no problems at all! I assume it is just the update but can anyone help? I've done everything-factory restore, cleared it of music, resynced with one playlist, hard re-set and everything...someone help!