Startup Failed with i2c connected

I just moved my Pixhawk from one frame to another, and now I am having trouble getting my Pixhawk to function.

When it boots up, I get the ‘Startup Failed’ Tone (link to sound). However, I have found out that if I unplug the magnetometer from the Pixhawk, it boots fine. If I look at the BOOT.txt file on the SD card, the only thing I find is ‘hmc5883 calibrate failed.’

I have tried re-flashing firmware both through the wizard and Install Firmware menu of Mission Planner 1.3.5. Both times, it was flashing ArduCopter V3.1.5 Hexa.

This is all with the following hardware:
Pixhawk autopilot (purchased Jan 2014),
3DR ublox compass/gps unit
3DR 915MHz radio set
3DR power module
FR-SKY D4R-ii Rx in PPM mode

Any help would be much appreciated.

I just realized, it was because my GPS cable was backwards!
6 pin connector goes into the Pixhawk. 5 pin connector end goes in all the way to the left of the GPS module.

I have three Pixhawk and three 3DR GPS/Compass modules and all three configurations have DF13 six pin connector/cables from the Pixhawk to the GPS/Compass module.
The only configuration that I know of that uses the DF13 five pin connector to DF13 six pin connector cable is the APM2.5/2.6 and the GPS/Compass module.
TCIII ArduRover2 Developer