Im using a JTAGICEmkII, STK500 Board, ATMega644 and AVR Studio 4. Here are the steps I use but the AVR does not run the code unless I disconnect the JTAGICEmkII in AVR Studio.
1) Build my program (F7)
2) Connect the JTAGICEmkII in AVR Studio.
3) The JTAG window pops up. I then Program the Flash Memory.
4) The code does not start running on the AVR. How do you start the AVR chip to run the code?
BTW: The code does run if I close the JTAG window and disconnect the JTAGICEmkII in AVR Studio.