BF if you want to use a bootloader, FF otherwise. The chip will fail
verification if it's either unprogrammed or programmed incorrectly. I
have had issues with the programmer not erasing the boot section before
overwriting it, but that does not seem to be the issue here as you're
writing to a blank boot section. I imagine that either avrdude is
sending the programmer the wrong command or the programmer needs a
firmware update. There are different write commands for writing to the
flash and boot sections of the xmega. I had to patch avrdude a while
ago to get my jtagmkii cable to program the boot section at all. Now it
can write it, but it can't erase it without an explicit chip erase.
Slightly annoying, but workable.
Unfortunately, looks like you're going to need to delve into avrdude
and/or your programmer, or get another programmer. Btw, the avrisp2
works fine and is like $35 from digikey IIRC.
Alex Forencich