Ok I thought it had copied the ArduinoISP sketch as the lights flashed and it stopped blinking but looking back at the output it shows
Binary sketch size: 5,444 bytes (of a 30,720 byte maximum)
Binary sketch size: 5,444 bytes (of a 30,720 byte maximum)
avrdude: stk500_getsync(): not in sync: resp=0xf9
I think perhaps the AVR MKII has damaged the arduino board too or vice versa. Both did exactly the same thing and worked till I tried to program then nothing happens with an error but the chip gets nerfed.
Well that was my last chip so now I'm going to try using just the AVRMKII with a nerfed 328p on the breadboard.