HS3 Plugins Spawning Popup windows

I had to restart my system today and when HS3 started up I got a separate popup command window for every plugin.

1. Plugins work as long as I don't close the popups.
2. Tried restarting, no change
3. Updated from 311 to 312, no change
4. Disabled all plugins, restarted, and then enabled a plugin - immediately got a popup.

Its like something that should be happening in background is now operating in foreground.

Any ideas or suggestions are greatly appreciated.

Regards,
Vector