I was messing around with the gnet flasher on my Windows 10 64-bit machine, when I tried to use the Gnet flasher it failed as I expected it to. Out of curiosity I opened diskpart in a command window, opened disk management, selected the CF card, and used the clean command on the CF card. Tried the Gnet flasher again, it finished, stuck the CF card in, and the game loaded and works. So I brought the CF card back to the PC and tried it again using the same procedure, put a different game on it, and stuck the CF card in and had the game load and work yet again. Tried a third time with another game and it worked again.
So this seems to be a way to use the gnet flasher on a 64 bit Windows 10 machine.