Try holding "S" during startup to determine your save data location, and rename or delete the Doborog folder. That's the only thing I can think of to try. Maybe try holding alt after an alt-tab and using the windows preview function to navigate to and make sure that the Clone Drone window is in focus. Also make sure it's allowed through any software or hardware firewalls. It seems to help if it has internet access, but I think it may be a matter of the operating system losing window focus for Clone Drone.
I hope some of that helps,