The system sees something is plugged in when I plug and unplug it:
bluehat@Matapan:/dev$ tail -f /var/log/syslog
Mar 23 15:36:35 Matapan kernel: [156082.1128
It turns out that Ubuntu will acknowledge that the object is there but not play nicely with it until you fix up some of your udev rules. Thanks to http://steve.kargs.net/bacnet/avr-isp-mkii-on-ubuntu-hardy/ which provided files that only needed a little updating.
Create new file /etc/udev/avrisp.rules
SUBSYSTEM!="usb", ACTION!="add", GOTO="avrisp_end"
# Atmel Corp. JTAG ICE mkII
ATTR{idVendor}=="03eb", ATTR{idProduct}=="2103", MODE="660", GROUP="dialout"
# Atmel Corp. AVRISP mkII
ATTR{idVendor}=="03eb", ATTR{idProduct}=="2104", MODE="660", GROUP="dialout"
# Atmel Corp. Dragon
ATTR{idVendor}=="03eb", ATTR{idProduct}=="2107", MODE="660", GROUP="dialout"
LABEL="avrisp_end"
Now create a virtual link to the file and give it a rule priority
cd /etc/udev/rules.d
sudo ln ../avrisp.rules 60-avrisp.rules
Check you're in the dialout group
groups
Restart udev
sudo service udev restart
Hooray!