JTAGICE3 problems with AS6.2 SP2

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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)

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I reinstalled AS6.1 SP2.

It did not automatically upgrade the JTAGICE3 to version 3.

I can now debug and program via JTAG to ATmega2560. I believe the JTAGICE3 is still at version 2.15. I will check tomorrow.

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Yes, JTAGICE3 FW version is still 2.15.

Works with AS6.1 SP2, except doesn't report JTAGICE3 version (in device programming) and doesn't upgrade from view -> available atmel tools. (reports fw up to date.)

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I have found trying to debug with SP2 to be really flaky. I can hit a break point, but not single step. The processor goes off into random memory locations. I am using an EVK1105 board that has been working ok.

I have tried a JTAGICE3 and an AVR One!. Both are flaky. I am using JTAG and Mictor connections. My processor is an UC3, AT32UC3A0512.