This is not a bug but rather intended behavior as they have now become modal instead of windows within FileMaker. If set you had a dual monitor setup, you could see that they can now be brought outside the constrains of the FileMaker Application Window.
Hmm, I just tried this on OS X 10.6.2 using FileMaker Pro 11 and the script windows do not behave this way. Why is this? This makes working on layouts and scripts simultaneously very difficult on smaller screens using Windows.
Thank you for your posts.
"mr_vodka" is correct. This is the intended behavior on Windows. Floater windows will always be on top of document windows. This change was done to allow scripting windows to be moved outside the application window.
Mac OS does not have an application window, so all windows are "floating", so this behaves differently than Windows OS.