I spoke to Pioneer Canada about this today, and they stated that they had not had any reported problems from consumers with regards to this problem.
The rep stated, after conferring with his product specialist, that the problem was more than likely with the ipod or the connection to the ipod, and not the head unit or cable.
I've had this ipod for a while (80gb video) but it worked flawlessly with my Clarion deck I just got rid of to pick up the F900, so I doubt it's an ipod problem.
Maybe if more of us complain to Pioneer, or if we get a list of people experiencing the same problem, we can go to them as a group.