I have the same ipod with about ~6000 songs on it. When I had the fusion SEL with sync it did the same thing. You can try unplugging the ipod and reset the sync and then plug it back in after the reset. Sometimes it works.
I now have the same ipod plugged into my 12 focus with MFT and it works flawlessly, all ~6000 songs available.
13 Blue Flame F150 FX4 402A on 20's loaded
13 Frosted Glass Escape Ti 401A loaded
13 Performance Blue SE 201A
14 Dark Side Fusion SE 200A
L-CCC #18/HOIA #37