Can't run example sketches on Intel Aero


I have been having trouble running the GPS_UBLOX_passthrough example sketch from the Ardupilot repository. I am able to build the sketch fine using the wiki fine but when I upload the sketch it messes up the firmware on the flight controller. I followed the steps on this page:

The only difference is that I don’t include the --upload command because the first time I did it something happened with the flight controller and I ended up having to reflash it. I open up a mavproxy shell through a TCP connection since for some reason I can’t do it through any of the serial ports and I tried running the example through there but that did not work. Like I mentioned before, I am on an Intel Aero RTF running Copter 3.5.7 using Ubuntu as the OS. Any help would be greatly appreciated