I have had loads of problems, tried taking all the music off (not a problem) but then wouldn't go back on.
I have just been on the phone to apple, and have fixed it, and was trying to make mental notes so I can post on here.
In iTunes, click View>show sidebar
Connect iPhone
On the iPhone menu, uncheck all apart from 'manually manage music and vidoes'.
On the sidebar, on the iPhone, press the small arrow on the left.
Select 'music'. You should either see nothing, or in my case, my entire library, but greyed out.
I then went back to my music library, selected one song, and dragged and dropped into the phone on the sidebar.
Apply
Sync
Then ALL my music went on with no problems (not just the one song I selected)
Perhaps if it doesn't work, select all your music (ctrl+A) then drag and drop onto the phone.
This is with an iPhone 5 running iOS 7.0.4 and iTunes 11.1.4.62 on Windows Vista.
GOOD LUCK!