I have to dig up what I did to get the Pololu programmer to work with the Arduino IDE. It was under Windows XP, and I am now running under Ubuntu 12.04 LTS. The XP partition is still there, but I'd have to search in the Arduino config files to see what I did.
It looks like you have your programmer correctly hooked up to your JBD board, though. I am assuming that you have your JBD board hooked up to a separate power source - the programmer will not supply power to the JBD board.
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