"You should write it with Arduino IDE. When uploading is done, wait for about 1s, there will be led light turned on (clearing EEPROM complete). Why don't you take MegapirateNG 3.0.1 R4 from github https://github.com/MegaPirateNG/ardupilot-mpng which…"
"Did you calibrated compass and gyro? You should also first write Clear EEPROM sketch (arduino examples) and then write arduplane. Had similiar problems."