I get some but not all of these warnings, which suggests that you have a different compiler version.
I have avr-gcc 5.4.0; can you try my .hex file? simpleserial-rsa-CWLITEXMEGA.zip (13.6 KB)
It sounds like there is an issue communicating with the target then.
One possible cause is SimpleSerial version mismatch: are you setting SS_VER in the notebook? You should not need to. The firmware I sent was compiled for SS_VER_1_1, which is the default; if you set SS_VER=SS_VER_2_1 in the notebook, then communication will fail due to the version mismatch.
Are you able to run any of the other notebooks successfully on your XMEGA target? If so that would eliminate most of the other possibilities (20-pin connector issues, improper setup on the CW308 board if you’re using that).
Are you using the CWLITEXMEGA board, or CW308 with an XMEGA target?
Now I do not set the version to SS_VER_2_1 and I am able to capture the trace for the hex file you have shared. However, I am still getting the old error when I try with my hex file.