I have had issues with the plugin scan taking forever. For me, it turns out that where the scan hangs, is the plugin which is causing the problem. I had to reinstall the plugin and select "reset" in the scan options. That fixed the problem for me.
 
I did discovered that MixBus 3.1 is the actual problem. When it locks up, it seems to corrupt plugins. Therefore, the next time I open up Sonar it has issues scanning plugins. Now, I'm back to treating my stems files in MixBus and not mixing.