using 4.16 (build 628)
I am unable to write to the boot section using this AVR Studio version. The chip is blank when reading the chip after programming.
When downgrading back to AVR Studio 4.15 (build 623) everything works fine. When reading the chip I can see the bootloader there.
Now if only I can get the last 3 hours of my life back, struggling to figure out why the bootloader wouldn't work but everything else did :P