I'm running a self compiled version of wine 1.1.4 on Suse Linux 9.3 and I've been totally unable to minimize any wine application windows at all. Clicking on the minimize button seems to make the application window flash a bit but does nothing. I can roll up/down, close and maximize/restore the window. And there is also the issue where the wine application windows automatically autoraise when the mouse travels over the window even though I've set the option of not having the windows raise up in the GNOME control panel. It happens only for wine application windows. I'm checking both options under window settings to allow the window manager to both decorate and control the windows.
