I moved your post to a new thread. We are currently aware of a bug that is causing programming issues when using Atmel Studio with our programmer, and we are working on reporting the bug. Could you try programming your 3pi using the following workaround?
- Compile your program using "F7".
- Go to Tools -> Device Programing.
- Select "STK500" under the "Tool" menu. The "Device" and "Interface" should then show ATmega328P and ISP, respectively.
- Click "Apply".
- Go to the "Memories" section and click the "Program" button under the "Flash" menu.
If this workaround does not work, could you tell me more about your setup? Do you have any additional things connected to your 3pi? When was the last time the batteries were charged or replaced?