I'm trying to fire up my version of AVR Studio5.1 to check - it doesn't seem to want to recognize my MKii since I changed the drivers for it to work with the IDE. Downloading 6.0 to see if that fixes it.
Sounds about right tho. Fuses look to agree with the settings in boards.txt:
mega2560.name=Arduino Mega 2560 or Mega ADK
That's why I do this in the IDE:
Burn the bootloader, which sets the fuses
Download the sketch via File: Upload Using Programmer, wipes out the bootloader, leaves the fuses, and the sketch starts immediately after a reset.