AVRISP mkII not reading device signature
There are several possible problems. One is actually udev. If it runs fine calling avrdude with sudo, you have to get your udev stuff right. In Debian Wheezy I have the following line in my /etc/udev/rules.d/56-avr.rules file:

# Atmel AVR ISP mkII
SUBSYSTEM=="usb", ATTRS{idVendor}=="03eb", ATTRS{idProduct}=="2104", GROUP="users", MODE="0660"


I guess you can change any appropriate group.

If that's not your error, check your circuit. A common problem is other things are connected to the ISP pin header. If you want to be sure, put the controller somewhere, where nothing else is connected to these pins and try to flash it there.

And finally: check the colors of the LED in the mkII. Errors or warnings are indicated by yellow/orange or red color. If everything is wired up correctly, the LED in the programmer is green.