I have a JTAGICE MKII programmer that shows up in the list of programmers in Atmel Studio 7 (latest version today). I select JTAG and click apply and it seems to be okay at that point, but when I click on the button to read the device ID, I get the error "JTAGID not valid. Debugger command enterProgMode failed." Here is the kicker though, there is no problem programming the board (has an ATMEGA1280) on my co-worker's computer. I did a fresh install on a 3rd computer in the lab, and it too fails to read the device ID. I am using the exact same board, same usb cable, same programmer, and I have not even moved the programmer's connection to the JTAG connector on the board.... so it is not a cable issue, or a board issue, power issue, or a 'plugging in the JTAG connected the wrong way issue'.
. I did not mess around with fuse settings at all, so they should be correct considering it is able to be programmed on that one magical (co-worker's) computer.
I have even tried installing the same exact version of Atmel studio 7.0.1417 as the computer that is able to program, using the same install exe file that my co-worker used!
I even have the same model computer as the computer that is able to program, and we are both running windows 10. Same USB cable is being used. I am using the same power supply brick to the power the board that contains the atmega1280.
I tried two other computers, and they too have the same problem programming (No copies of atmel were on those computers so there is no version conflict to speak of).
I haven't used Atmel Studio in the past much, but I am NOT impressed.