Spent a couple hours trying to sort this out. Restoring the system to an earlier date did not solve the problem. What gave me a clue as to the root cause of the problem was when I disconnected the VS100 from the computer and deleted the VS-100-1 Control Surface settings. I then connected another Control Surface, (a small keyboard with ACT capabilities). After entering all the info, clicking "apply", closing the preferences, saving the file, I closed Sonar and then reopened. Interestingly, when I opened up preferences, the Control Surface was still showing the VS-100-1. This told me that the file that stored the Control Surface settings was derelict in its duties.
I found the file (ctrlsurface.dat) renamed it and then copied the same file from my previous version of Sonar (X2) hoping that it would be the compatible with X3. (I was still using the VS100-1 back then too). I inserted in the folder where ctrlsurface.dat is stored, opened up Sonar and voila, it is all better.
Now back to music making...
Walt