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I repeated several times with 2 firmware files, one was from 3-dr and another one was our own, it didnt fail if I manually reboot solo. It failed sometimes if I use loadPixhawk.py even with run-level management. It also failed sometimes if I reboot the system with command \"shutdown -r now\". It seems the system has to be powered off before flash the firmware. \r\n\r\nPlease test it and tell me if it wont work on your system. 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