http://bugs.winehq.org/show_bug.cgi?id=34315
--- Comment #12 from Vincent Povirk madewokherd@gmail.com 2013-08-21 13:36:46 CDT --- Wine does very little z-order manipulation and instead relies on hints to the window manager. Trying to enforce the exact z-order semantics of Windows hasn't worked well with window managers, which also expect to control the z-order.
The exception to this is that we raise a window when it becomes the topmost Wine window: http://source.winehq.org/source/dlls/winex11.drv/window.c#L1225
So it's not clear to me why HWND_NOTOPMOST would move your window behind anything, unless you're triggering a window manager behavior. Some window managers have protections against programs that spontaneously raise or steal focus. Does the same thing happen in a virtual desktop?