I have bought 4 Pixhawks (not at the same time)
2 out of 4 have had the same problem that firmware cannot be uploaded via mission planner and only via px4ploader.
It looks that it is possible to upload via APM planner although that way it leads to the unit being unable to connect via either telemetry or USB which probably means the firmware update has been unsuccesful and APM planner has not raised an error.
Again to sum, only using command prompt px4uploader it is possible to upload firmware and this is true only for some units but not others.
Thanks