We put together a ChipworkX updater application. It will erase the device then update TinyBooter and Firmware from the SDK.
So when the firmware needs to be updated, just run this application. No need for a command prompt or MFDeploy.
Hopefully, this will make things easier.
UPDATE
The ChipworkXUpdater.exe is now part of the GHI NETMF and .NET Gadgeteer package. Which is #3 under system preparation.
This is now part of the SDK
Good!
Woooo yeah 
Now all my devices can be updated easily.
By the way the usbizi and emx updater work absolutely fine
I am happy ;D
Hi,
Nice tool, and I would love you guys to improve it by adding the possibility to select an “Application HEX file” to do a complete system install.
It would be great for deploying many units in a short time - complete with the ISV app installed.
And while you are at it, you could do something similar for EMX 
Best regards,
Ronny
I believe you can select any files to download. Put the firmware and the application files in the same folder and select them all together. It should work. Let us know if you have problems.