I'm using 11.19 on Windows 10.
Can you be more specific?
After investigating this, it seems that Windows 10 forces windows which do not have taskbar buttons to appear on all virtual desktops. Currently, Microsoft have not provided any API to override this.
(There is an API to move normal windows between virtual desktops, but there is no way to prevent Windows 10 from assuming/misinterpreting certain window styles or parent/child situations mean a window should be on every desktop at once. Those styles and situations have existed for decades and have other meanings which have now been overloaded with new semantics, which aren't always wanted and which cannot be turned off.)
There are some virtual desktop enhancements coming in the Windows 10 "anniversary" update, although I do not know exactly what they are. We will keep an eye out for APIs which allow us to control this better.