It works fine to program the 3pi with AVR Dragon via the ISP.
But is there some way to make the right wheel of the robot not spinn when the Dragon is connected to the 3pi. (When the programming dialog is started in AVR Studio 4 the wheel stops to spin.)
One of the mega168’s motor control lines happens to double as an ISP programming line (since this programming line is one of the mega168’s hardware PWM outputs), so a programmer that does something with this line without holding the mega168 reset will drive one of the motors (reset is connected to the motor driver’s suspend line). Apparently, unlike most other ISPs out there, when idle the AVR Dragon is pulling its programming lines to a voltage that makes the motor spin. The only way I know of to get around this problem would be to use a different programmer, or to hold the 3pi’s reset button while you plug in the programmer until you bring up the programming dialog.