I looked at the firmware code from high level and would have some ideas where to start debugging, but that will take some more of my precious time :S And I don’t have a programmer yet, would need to buy one myself (and shipping times to my place are evil)
So if someone could help with debugging that would be great
so just to be sure, I ordered another BrickPi from a different distributor, and even an replacement Nxt Color Sensor (Lego 9694, http://shop.lego.com/en-US/Color-Sensor-9694) as well. The BrickPi seems to be same as the first one, board version v2.8, firmware v2. And no change, still running into exact same issue, the color sensor only initializes and works with the earlier described workaround initializing both ports of a given arduino, where the color sensor is attached to the first port (S1 or S3). Still waiting for an AVR kit to be able to look at the firmware.
Since detailed documentation is rare, would anyone who got the color sensor to work (calling John@Dexter) be able to show a debug log of the serial comm incl. timing. As this is plain serial, my idea is removing all the boilerplate code and just sending the required byte[] and timing.