I never had any issues. I have both my 160gig ipod and my iphone4 synced. I now leave the ipod permanently plugged and if i want to listen to my iPhone I listen to it off the bluetooth. If you are still having issues after lovemystang22's suggestion, I suggest you pull out the sync fuse for a minute and let it reset. if that doesnt do the trick, I would focus on the iphone. My sync acts up sometimes ands after I reset it via the fuse it works perfectly.
There are also forums on the syncmyride.com website that may also have helpful answers.
Ordered: 2.21.12 VIN: 3.23.12 Build: 4.13.12 ETA: 4.22.12
2013 GT Premium. 6MT. Deep Impact Blue. Recaros, Nav, Track Pack, Reverse sensing, Backup Camera. Borla S-Type Axlebacks, WeatherTech floor mats, Ford Racing K Springs, BMR Adj. Panhard, Upper and lower billet grille.
12.10.2011 RIP: 2012 GT Prem, Kona Blue, 6M, 3.73's, reverse sensing package, premium wheels, Grabberpony Shift Knob, WeatherTech floor mats, BOSS valence and splitter, Saleen Grille, HID's, Roush Axlebacks.