It seems to me that the iPod issue is a software issue. There is obviously a connection, physically, and the hardware all is in good working order. It seems that during boot-up, if the iPod is on, it will more often than not magically disconnect itself once the unit goes into map-mode, or your bluetooth phone connects to the unit.
I have found a sort of a fix, however. Before I turn the car off, I go to a/v input, and select "Off".
Then, when I start the car, I give the head unit a ridiculous two full minutes to boot, and I don't touch anything...I don't touch any buttons, maps, or