Hi Jack,
umm Yes your (neater) code does a similar thing to the rubbish one I wrote :), I can't use that core as I have a USBtinyISP and I am not sure it will work with the 644 and can't get my Atmel Dragon working as Studio won't run at present (Atmel technical are working out why for me at the moment).
The core I do have is a modified sanduino, which seems old news from what I can see on the net. but at least it works ???? well maybe not as we might be finding out. Out of the box I had to edit it to use the 644P properly as it left the Jtag enabled and I need those pins.
Might it be a fuse setting?
Steve