Well, I know I can't upload kernals/firmware while docked in my component box. However I never bothered to find out if I wired it wrong or something else is at fault.

That's an easy one to fix.

When docked in-car, the serial port is slowed to 4800bps for compatibility with certain other in-car devices. If you want this to change back to 115200, you can do it in config.ini. Check riocar.org for dox on this subject.