https://bugs.winehq.org/show_bug.cgi?id=34631
--- Comment #24 from jubilantjerry@gmail.com --- I've found a workaround in my instance of this bug. If I use an Ubuntu keyboard shortcut to minimize the application window showing the drop shadow problem, then the drop shadow no longer lingers on top of all windows even after the main window is restored.
After starting the application fresh, if I use the minimize button that comes with the application window, the drop shadow is gone. But the drop shadow will come back when the main window is restored. If I use the keyboard shortcut, then the drop shadow never comes back, regardless of how I restore / minimize / resize the same window afterward. New windows created by the same application may still show the drop shadow. Not all windows respond to the Ubuntu shortcut, which is kind of annoying, but having the main window be responsive to that is already a nice improvement.
This leaves me with a couple questions: if the drop shadow is behaving like a window, why doesn't it appear as a separate entry in the dock like other cases when an application has multiple windows, and why does the keyboard shortcut handle this differently from pressing the minimize button?