Did you happen to have your antivirus software running while Sonar was installing? I had a couple of times in the past where I had post-installation issues with a Sonar version (either X1 or X2, cannot recall which), and when I did a reinstall, with my antivirus suspended, everything worked fine after that.
I think I may have been running AVG at the time - I have switched to Avast since then - smaller memory footprint and better overall, and free.
But it might be worth a shot to try a COMPLETE removal of X3, followed by a temporary suspension or termination of your antivirus/anti-adware software, and then an install of X3.
Doing the uninstall and a clean install would not adversely affect any of your projects, so it shouldn't hurt anything.
Are you running X3e? That was the most up to date maintenance level for Sonar X3. If you are not currently running with the 'e' maintenance release of X3, you do not need to install the a, b, c, or d maintenance, just download and install X3e over whichever maintenance version of X3 you have, or if you do the uninstall and install of X3 then just run X3e right after that.
I will be out of town for about a week, leaving in about an hour for the airport, but I will try to pop in when I can and see if the above worked or try to further assist as I can.
Bob Bone