I upgraded to AS6.1 build 2730 AKA SP2. When I attached my JTAGICE3, AS6.1 SP2 automatically upgraded the JTAGICE3 to FW version 3. I could not debug with DebugWIRE. Atmel provided me with a downgrade for the JTAGICE3. I applied this downgrade and the JTAGICE3 worked, but seemed to have some issues.
I downgraded my Windows XP machine to AS6.1 build 2562 and the JTAGICE3 issues were resolved for what I was doning. (Debug ATmega328P with DebugWIRE and ATmega2560 with JTAG. I also was successful with ATxmegaA3BU with JTAG).
I decided to setup a test Windows XP machine. Previously it had AS6.1 build 2562 installed and worked as above. I downloaded the smaller installer (not the full) and this time I didn't remove the old Atmel AS6.1, just installed.
I attached the JTAGICE3, expecting it to be automatically upgraded to FW version 3. It was not upgraded.
AS6.1 saw the JTAGICE at the project properties window, but I could not use to debug, ATxmegaA3BU via JTAG, nor program, also at the view -> Available Atmel Tools window, It was listed, but I could not ugrade from this window.
Moving back to my AS6.1 build 2562 machine I verified that the JTAGICE3 was still at FW version 2.15.
What I would like to do is upgrade the JTAGICE3 to FW version 3 again. (I know I will have to upgrade and downgrade to move the JTAGICE3 between the environments, but if it makes sense to use AS6.1 SP2, I could buy another JTAGICE3)