I had a similar experience. The instructions don't direct the installation to be performed from the /pi/Desktop folder.
I worked at this quite a while and was successful in installing onto a 8GB card and was able to upload to the ArduBerry the Blink sketch on that card.
However, I have not been able to duplicate this on a 32GB card. I've formatted & reinstalled a fresh current (01/11/17) version of jessie. I found that, even though Arduino IDE was installed, the Arduberry installer did not find it and proceeded to install 1.6.1. The Pi did find the ArduBerry but wouldn't upload through the programmer with pretty much the same error as the OP.
I tried it again, this time formatting & imaging the recent jessie and running the install without having the Arduino IDE already installed. Now I have two ports to choose from (/dev/ttyAMA0 & /dev/ttyS0) and neither of them work. Still can't upload using the programmer.
I still have an error consisting of "avrdude: AVR device not responding arvdude initialization failed, rec=-1 Double check connections and try again, or use -F to override this check"
Where can I find this option to use the "-F" override?