As I mentioned in a previous post, since upgrading my iPhone 5 to iOS 7, synchronising using iTunes has become really buggy. Try googling “itunes sync hangs waiting for changes to be applied” and you’ll see I’m not alone.
A lot of the time, syncing happens fine, but sometimes it will do bizarre things. For example, I had a 10 track album where 7 of the tracks had just an “Artist” name entered in the song data, and 3 tracks had both “Artist” and “Album Artist” set to the same value. On my iPhone, the album only showed the 7 tracks where the “Album Artist” field was set. After clearing the “Album Artist” on all the tracks, the album then showed up correctly on the iPhone.
Also on random occasions, the sync process seems to hang at the “waiting for changes to be applied step” and then after about 20 minutes want to re-sync thousands of my songs to the iPhone for no apparent reason.