Hi,
I have loaded the hex file through atmel ISP programmer through atmel stdio 6.2 in atmega2560 and atmega16u2 and it was successful also without any error.
I tried to check even by erasing the code from the atmega2560 to check the L led response it was staying "ON" continuosly but not blinking on reset .
Then again i loaded Hex file "stk500boot_v2_mega256.hex for atmega2560" throgh atmel isp programmer and again it started blinking but still when i load a simple blink program through arduino via USB cable it is showing me the same error.
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: stk500v2_getsync(): timeout communicating with programmer
Programamer i used is:"AVR ISP Programmer"
Regards,
Vipin