Adding this comment:

I have the impression that this my problem is mainly a documentation issue.  It concerns obviously all tool windows that can be open thru the View>Toos menu of EiffelStudio.

My newest understanding is that after opening a tool one is expected to place it into a Layout pane and use it from there, not as a standalone floating window.

But I am still baffeled that the Active Windows window at times opens as a floating window under Windows itself. I have not found a way to get the other tools to appear in a standalone window. Did I miss a Preferences setting, or have I maybe altered that setting by mistake?