I am attempting to communicate with the arduberry on a raspberry pi 2 using java and jSSC-2.6.0. I have created a little test program and a sketch based on your examples. I wired an LED to pin 8 (I too figured out the PIN 13 problem) to indicate that the arduberry received the communication from the RPI. The data seems to send fine as the LED lights when it should, but I never get the correct response from the arduberry. I setup a SerialPortEventListener to read and printout the response on a RXCHAR event when the eventValue equals 10. Nothing is written out. I did some debugging in the java program and determined that I get one response of only 4 bytes, not 10 and it is gibberish.
I also tested the communications with your python program and it worked perfectly, so there is something wrong in the java program, but everything seems fine. Is there some configuration or parameter that is unique to the arduberry serial communications that I need to allow for? I really would like to get 2 way communications working in java, so any suggestions would be welcome.