We are having a weird issue, where our code runs fine if we use "debug and break" or "start without debug". But if we try to just program the chip, the program fails to operate properly. Uarts don't work, button presses are not read, ect.
Once programmed with "debug and break" or "start without debug" we can power cycle them and they still work fine. All three methods pass verification from the programmer tool and the project hex file.
Why would they be different? I'm using the AVR dragon in jtag mode on an atmega64a.