Pixhawk Stops working after uploading Firmware

I’m trying to upload some custom firmware from ArduCopter V3.5, but after it finishes programing, it flashes red for a second, and the LED does not respond. It works fine when I upload ArduCopter V3.6.9, and the custom firmware works on other Pixhawk’s I’ve tested. So far I’ve…

  1. Inserted a properly formatted SD Card
  2. Uploaded different Ardupilot variants (Plane, Heli) then reflashed the custom firmware.

What other ways can I troubleshoot?

Edit: Rolled back to ArduCopter 3.5 from the master branch, and I’m still getting a irresponsive Pixhawk.