Ok, using the HEX and BIN worked like a champ. My program basically used the "Erase Firmware" from MFDeploy, then Uploaded the new HEX and BIN files, then verified the firmware version was different than the previous version. Finally it sets the MAC address (as this gets erased) and reboots. Everything comes up fine and it's showing version 4.2.2.2 and the Pandora's Box version 2.95 software was still on there and didn't need to be erased as it doesn't affect those sectors.
All in all, the process too about 2 minutes. This is a great way to allow end users of my product to get firmware and software upgrades alike.
Would it be possible to elaborate on the steps to accomplish this? I've tried the "standard" upgrade method described at the beginning of the post (StDfu Tester doesn't seem to find the Netduino, whether I've connected it WHILE, or WHILE NOT pressing the button). I also tried your method, finding the Erase | Firmware (I included Deployment as well), then trying to upload the .HEX, followed by the .BIN files. All this resulted in was:
Tinybooter.hex:
Unable to deploy to device
Invalid address 8000000 and range 9c04 Ram Start 0, Ram end 20000
or
TinyClr.hex files ("ER_CONFIG" "ER_FLASH"):
Unable to deploy to device
Invalid address 800c000 and range 90c Ram Start 0, Ram end 20000