I use Guitar Rig with MainStage as well, I and I can confirm that after speaking with the MainStage Team at Apple, Guitar Rig is the offending source of not recognizing your GIO, not MainStage. I have also made NI aware of this, but have not had any return info.
I have found that 98% of the time when this happens, I have turned off/disconnected the audio interface before the computer has finished it's shutdown, so make sure to shutdown the computer completely then power down/disconnect your audio interface.
If it should happen again, here is what you do- Go to your Hard Drive/Library/Audio/Plugins/Components/ and drag your Guitar Rig X.component (X being whatever version of Guitar Rig you are using) to your desktop. This will make a copy of it there. Next, trash the one in the Components folder (you may need to enter your password to do this) and restart your computer. Upon relaunch of MainStage, you will get the notification that the plugin is missing, disregard this and let MainStage start. Reassign your Gio as your audio interface in the Preferences and quit MainStage. Now, go back and return the "Guitar Rig x.component" file to the Components folder and restart. This should take care of the problem.
I have used MainStage with many clients for hundreds if not thousands of shows with a zero failure rate (other than human error)
Ashermusic and mmm42- you can also add K.D. Lang, Journey, Def Leppard, David Paich with Toto and Rush.
Scott A.