As it was four months ago you may not remember, but . . .
1) Did you ever tell it to program using the MKII with it set to program something other than the ATMega128RFA1?
2) Did you ever try to program it without it being powered up (ie forgot to plug a battery in, or a battery with a low voltage, or at least not plug in USB, etc)?
3) Did you try programming it above 4MHz?
4) Did you accidentally unplug something while it was in the process of programming?
5) Does your MKII program your other microcontroller without any problems?