I am just saying the ICSP near the usb port is for the 8u2/16u2 and the other one is for the mega2560. The bootloader goes into the 2nd one. The first one: http://arduino.cc/en/Hacking/DFUProgramming8U2
To fix mine, I use avrdudess and that cheap avrasp, first plugging it into:
Without connecting the usb or power (only the power provided by avrasp)
(This is if the serial port isn't working properly)
Later on, if the serial port is present but I can't send a Sketch
, use this other connector with the avrasp:
Wait 1-2 mins and the board starts to blink and everything is ready.