"Why do you need to run the Cleanup utility? It is only intended as a last resort for issues with installation."
Well, I was under the impression that it was best practices. Guess I was wrong and now I'll pay the price. Should be more obvious that everything will be blown out by the routine. i.e. STOP - ALL TEMPLATES WILL BE LOST - DO YOU WISH TO CONTINUE?
On a positive note, the program seems much more responsive now.