So by changing the programmer from arduino to stk500v2 I was able to reproduce yesterday's results for Mega number 2. I used the following command:
avrdude -C "C:\Users\Gaurav\Dekstop\Gaurav\summer job\arduino-1.0.1\hardware\tools\avr\etc\avrdude.conf" -c stk500v2 -p m2560 -P com11 -F
to get:
avrdude: stk500v2_getsync(): can't communicate with device: resp = 0x01
avrdude:stk500v2_command(): unknown status 0xc8
avrdude: initialization failed, rc=-1
avrdude: AVR device initialized and ready to accept instructions
avrdude: Device signature = 0x000000
avrdude: Yikes! Invalid device signature
avrdude: Expected signature for ATMEGA2560 is 1E 98 01
avrdude: stk500v2_command(): unknown status 0x01
avrdude: stk500v2_disable(): failed to leave programming mode()
avrdude done. Thank you.
I'm really stuck here, any help would be much appreciated.