I don't use an iPod but have a 32GB thumb-drive instead. I have noticed that I get an occasional skip or pause while playing music via the USB thumb-drive. I'm not talking the pause between tracks but in the middle of the track.
I'm guessing that the uP is busy doing something else and resumes playing when complete with whatever it was doing. If so, that would suggest the uP is pretty lame power/speed wise...
2012 FF Ti HB Sonic Blue, Built 5/7/12, 401A + Parking Technology Package and MFT w/NAV 3.0.2 -> 3.2.2 -> 3.5.1 -> 3.6.2