All I did was verify the firmware version of my camera, copied the firmware file to an SD card (formatted in the camera) and followed the rest of the instructions.
This may be a key piece of information here. Have others that have had this issue used the SD card or the CF card?
For those that were able to do the upgrade what did you use?
Additional information from my upgrade:
1) I had a non-Canon battery (Maximal)
2) My battery charge was 1 bar (didn't pay attention to it), at end of upgrade, my battery indicator was blinking
The only reason I used the SD card is because the SD card in the slot didn't have any pics. My 40mm lens was preordered so I got it soon after it was in stock. As others have speculated, it may be that some lenses do not have this problem. I never had the physical problem of having to reset the lens. It always worked fine for me but then again, I pack and use my stuff very gingerly so I may not have had the correct conditions for the problem.