http://bugs.winehq.org/show_bug.cgi?id=34315
--- Comment #7 from Lope lopeonline@gmail.com 2013-08-21 12:32:07 CDT --- A HWND_TOP window can only be on top of other HWND_TOP windows IF it's in focus. Simply setting HWND_TOP on a window actually does nothing besides clearing HWND_BOTTOM. You need TOPMOST to make it the most top window, because all windows are HWND_TOP. The value of HWND_TOP is 0. Its probably default when you create a window with pure API.
To be really explicit: The wine bug is simply setting HWND_NOTOPMOST makes the HWND_TOP window fall behind another HWND_TOP window that is in focus.
I expect this is a logic difference with how windows are positioned on Windows vs Linux.