You should be able to do that with Windows also. The commanrd is

"flasher -c -F main.bin -F emmc.bin -f -R"

Another command you could try is to full initialize the device filesystems:

"flasher --erase-user-data=secure -F main.bin -F emmc.bin -f -R"

However, if the problem is the USB porst of your computer, like @pichlo suggested, then you need to try with another computer.
(and finally, if nothing else helps, try with Linux... For example get an Ubuntu Live CD image, boot with that and install the fasher DEB packet...)