Steve,
Yeah, I agree. The debugging messages are still in there if you want to use them, but they kill the serial connection. They do work with the Ethernet connection though. They ARE sort of pointless if using the Serial connection to JMRI though. I would say enable them for the Ethernet connection, but disable them for the Serial connection. I think that they might be useful for users getting everything connected and set up, but after that... I am looking forward to you connecting as many readers as you can (6 for the Uno)!
Tom