Brett, did you ever get a fix to your problem? I am having the same issue while building my home dock... I see output from the serial port, but I cannot enter any data through the serial port. I have car_rate=115200 under the [serial] header in config.ini, and pin 5 on my serial port is grounded with the large ground pin on the docking connector. Not sure what else to do here.
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Mark Cushman