I am having similar issues, I had posted this on Terry's forum:
http://www.n54tech.com/forums/showthread.php?t=16554 but did not get any responses.
today I read codes and got the "CD87 PT-CAN communication error" code which shows up randomly, I normally just get these tuner codes: 3106, 28A0, 2C90.
My issue is random, but sounds similar to what is being reported.
Let us know how it goes with the new board!