Mine (1st-Gen iPod Touch) always does this. I've had no issues with the cable on any other device so I don't think it's an iPod hardware problem.
There's also a strange interaction that nobody at Ford can figure out (tho it's resulted in one new APIM to date...) which is that listening to my iPod causes random SD Card Faults, which kills my Nav as well as USB audio. I can't usually get the USB audio back until a complete MFT (performing maintenance screen) reboot but the Nav returns in about 15 seconds. This has occurred under v2.11, v3.0.2, and now under v3.2.2 of MFT.
I still wonder if there's a hardware problem with the "media center" in my center console...
2012 Focus Ti Hatch | Ingot Silver | 401A, Nav, Winter Pkg, Moon Roof, Parking Tech. Pkg
Build Date: 12/2/2011 | New APIM: 4/4/2012
MFT: Factory v2.11, 3/14/12 Web -> v3.0.2, 9/24/12 Web -> v3.2.2, 1/24/13 Web -> v3.5.1, 8/13/13 Web -> v3.6