I did the same thing when I bought mine, loaded up Atmel AVR Studio 5.1
But that loads up a Jungo driver.
The IDE can't use the MKii with it.
I had to go into Windows, uninstall the Jungo driver, and install with the IDE files.
Now I can burn bootloaders and upload sketches with no bootloader (File:upload using programmer) with the MKii no problem.
(search the forum for Jungo, someone else had posted about doing the same, I followed that - you might even find my post where I linked to the earlier post)