In Linux, you can actually bypass the updater program (it’s just a GUI) and run command line directly. The command that it runs internally is:
avrdude -c usbasp -p m644p -U flash:w:xxx.hex
where xxx.hex is the firmware file name. Make sure you are flashing the correct firmware (for example, if you have hardware 2.1, all available firmwares for that version are under the OpenSprinkler_v2.1 subfolder). Just enter bootloader, and run the above command. The updater is simply a GUI wrapper for the above command.