I have never worked with the Ardupilot, so i had a look at this page
It looks like the Ardupilot uses the TX and RX pins on the Pi. These pins are also used by the GPS on the BerryGPS-IMU., and you can only have one device talking to the Pi by serial.
The IMU, should have no problem working as it looks like the i2c pins are free
Mark --OzzMaker.com --