Hey Twyrick,
Try using a pass through 5V power adapter to power up the iDevice from an accessory line as soon as the car is turned on, that way the radio/entertainment unit can "see" the device immediately. If the device has to acknowledge the DC source, then recognize the USB port, then send it's HID to the USB port's micro, then finally be registered, you've already lost the opportunity to get connected.
Screwy I know, but that's been my experience. On my 2009 Navi unit I have to "Pre-Power" the iDevice before the stereo (with tap into accessory power line) then it sees the iDevice every time.
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