[Bongle]

We had this problem.

1) Make sure your USB stick is completely clean, except for the update file (this may not be necessary, but ours was clean, so it may have had a hand in our success)
2) Make sure your DS is in AUTO mode
3) Make sure the USB stick is in and it is in AUTO mode when you boot it.
4) Reboot the DS
5) Run the flash update process.

The last thing we did before it worked was trying a power cycle with everything plugged in and the DS in auto mode. Previously we had just tried flashing with it in teleoperated mode, then switching to auto. The mode switch apparently didn't take. Finally, we did a power cycle with the USB stick in beforehand. The documentation notes that it doesn't take hotplugging.

Hope this helps.