The issue you’re having has to do with the Arduino Libraries being out of date. You can update the library code to work with the newer ATmega328s on the 3pi as described in this post:
However, I strongly recommend using AVR Studio and our newer Pololu AVR libraries. With some of the newer functionality added to our library (e.g. serial and digital I/O), there really isn’t anything to be gained from the Arduino IDE anymore.
I’m using Arduinos along with the Orangutan so using AVRStudio would mean using two different environments. Probably more than my ancient brain wants to deal with.