I know you fixed this issue when the Kantu is loaded in the side panel.
But in V9.2.9 my scripts using prompt command opens now a second external IDE windows when I run kantu in the external window with prompt command. Basically the behavior your fixed in the side panel now shows up when you run kantu script with prompt command in an external window.
As I wrote, it was fixed running in a side bar but it broke kantu running in its own IDE window.
Also note: If I close the newly popped up window (in the background), the script will not continue executing after pressing the [continue] button.