Most people don't realize that the disc DOES NOT read that settings of the WiiKey. These are merely default settings. As long as you hit Save Settings and hear the drive spinning, you saved the settings. You should try to load a region backup and prove yourself wrong.
the setup disc is merely a gc bootable. anyone with a wii that's modded or gc will read and display the contents of the disk. however it will not write the settings for non wiikey users. I don't know and would not even attempt to try and write the settings with another chip, It might mess things up.
Where did you folks order your chips from? The Wiikey team has confirmed that there are at least two different "clone" (ie. counterfeit) versions being sold by non-official resellers. One of them, I am told, does not work with the configuration disc.