http://bugs.winehq.org/show_bug.cgi?id=11026
--- Comment #2 from Dmitry Timoshkov dmitry@codeweavers.com 2008-01-04 02:51:22 --- Below is the result of an investigation while playing with attached test.
The problem under Gnome is that the WM doesn't activate a window with _NET_WM_WINDOW_TYPE_UTILITY type. You have to click on it, then Alt+F4 works. Once I comment out assigning _NET_WM_WINDOW_TYPE_UTILITY to WS_EX_TOOLWINDOW windows in dlls/winex11.drv/window.c there is no need to click on a window, and Alt+F4 works without additional clicks.
Perhaps in that case we need to set input focus manually without relying on WM to do that.