Programming Arduino Atmega2560 with STK600 and Atmel Studio 6

Hi Everyone,

I started programming prior to Arduino's popularity, and initially began using AVR Studio 4 with an STK600 kit interfaced with an ATmega2560.

I am currently working on a project which was set-up using an Arduino with an ATmega2560. Anyone familiar with Atmel Studio 6 will know about the device programming window, where one can select the tool (STK600), device (ATmega2560) and interface (ISP).

Here is the issue, I have connected the ISP port on my STK600 to the Arduino's ICSP port, and using the device programming window in Atmel Studio, I was able to read the device signature and consequently read/write to the ATmega2560 flash memory.

The problem is that, even using basic debugging techniques like lighting up LEDs to see if board is functioning, the arduino doesn't respond although the ISP interface confirms the device signature and the program was correctly built and flashed to the memory.

Am I missing something here? Should the program be flashed as an Arduino sketch rather than compiled in C using the "regular" Atmel Studio protocol? Should I use another interface to interface with the Arduino eg. JTAG? Why is the Arduino irresponsive although the STK600 is able to interface with the ATMega2560 successfully?

Thanks