Greg, if you have any Waves plugs, that IS the issue with the scan not completing.
The scan always worked for me until a recent Sonar update. (can't remember if it was JP, I or H)
My scan would stop in X3 as well as Plat. (the same scanner) It ALWAYS hung on a Waves plug until I uninstalled and reinstalled Waves with their "new" installer interface.
Oh yeah, I also removed all WaveShell dlls I could find before reinstalling. There were quite a few spread around my drive.
HTH