I am reporting about a serious bug in AVR Studio 4.16 (build 628).
It is unable to write to the boot section.
AVR Studio 4.15 (build 623) however works fine.
Now if only I can get the last 3 hours of my life back, struggling to figure out why the bootloader wouldn't work on the Axon but everything else did
edit: Its fixed in the beta, along with two more bugs related to the ATmega640 (the Axon mcu):http://www.avrfreaks.net/index.php?name=PNphpBB2&file=viewtopic&t=78424