There may be a bunch of things Vera attempts to do; when any one of those fails, she considers the device ‘not configured’. It does not necessarily mean that a basic on/off does not work. I suppose only the logs may give a clue as to what it is that failed.
I wonder if your particular situation is triggered by not having the scene controller part of the VRCS2 device.
In your current environment, do the LEDs on the VRCS2 function properly?
Also, with some devices, including the 4-button Leviton zone controller, I’ve had them in a state where they would not function / respond properly (in my case: zone control worked, but not the LEDs!) and the only thing that helped was cycle the power to the device.