I have been unable to connect my JTAGICE mkII to a custom Xmega32A4 board but my Dragon works fine. The errors messages with the JTAGICE are:
Failed setting JTAG clock parameter
Failed to load debugee: ...\test.d90
The project debugger file 'Test' could not be written
My JTAGICE is marked "A09-0041" and App Note AVR1000 states:
Please note that your JTAGICE mkII should have a serial number that starts with "B0" or be marked with "A09-0041" for PDI to work.
All references to this from Google searches mention only the "B0" s/n and have no mention of the "A09" s/n so that is suspect. The JTAGICE still works fine with Atmega/Attiny boards. Any solutions?