So, my last complaint with the F series has been that it has been dropping my iPod constantly on bootup about half the time. I got my F700BT a few days before Halloween. My iPod didn't drop once until the 4th day or so. Then it dropped continuously atleast once every day upon bootup.
For the past two days, I have gotten in and out of my car about 10 times a day and the iPod was picked up EVERY SINGLE TIME. I also noticed something else... I noticed that I have not had my SD card in the unit either. I also did not start leaving my SD card in the unit until about 4 days after I got the unit. So, for me anyway, taking out the SD card has totally fixed my iPod problems. And to double check this, I put the SD card back in, booted it up and sure enough, the iPod was dropped by the 3rd bootup trial.
My theory is that the problem lies within initialization of all the sources on bootup. From what I can tell, the order of when the SD and iPod get initialized affects how the system sees the sources. The SD card reader in the unit probably runs off of the internal USB controller, much like the SD reader in my home computer. After all, the AVIC is just a Windows CE computer.
So, if the SD reader is running off of the internal USB controller AND as we know the iPod also runs off of the USB controller of the unit, therein lies the problem. The initialization of the SD as a source on bootup is screwing up the timing of the control commands sent out to the iPod.
So if anyone else has a recurring issue with the iPod not being recognized on bootup, try removing your SD card and see what that does. It does make sense though that it would be a problem with the timing of the USB initialization since every time the iPod drops, it works again right away when you unhook the reconnect the USB cable. That's my theory anyway.