I had an issue like this where a blank cmd prompt would constantly pop up every 1 to 2s, when i first started running Gunbot. Made it impossible to look at anything gunbot was doing.
Try a fresh download/upgrading to the latest version, make sure the firewall is allowing both the GUI and the normal .exe connections to the Internet, and give them admin access. I honestly don't know what I did, but it resolved itself. I believe it was a firewall setting change. :/