Probably not your case, but if parameters are set correctly in Mission planner and GPS pug is pointing forward in line with the flight controller, there is a chance that the module itself was factory installed inside the housing incorrectly. I’ve read once on the Pixhawk Facebook page of someone who had the same problem and it turnout that the GPS/Compass module was mounted incorrectly inside the GPS module housing. Probably not your case but if nothing else fixes it it is worth checking.