I'm in the same boat as these other users using a rpi2.
Fresh install of Raspbian for Robots, fresh update of all DexterInudstries software, rebooted.
Launched arduino IDE, loaded blink - wired up an LED for pin 13 and it worked great. That was the last sketch I could ever send to the Arduino.
Here's my output of avrdude:
pi@dex ~ $ avrdude -c gpio -p m328p
avrdude: AVR device not responding
avrdude: initialization failed, rc=-1
Double check connections and try again, or use -F to override
avrdude done. Thank you.