For some reason, once you enable the wine desktop globally, you can't seem to disable it for certain apps. What you can do is launch wine with the command to run the app in a virtual desktop. For instance, if you normally ran wine with "wine app.exe" you would now do "wine explorer /desktop=appname,1024x768 app.exe" with whatever resolution you wanted. If you want to do it with a game shortcut, you can easily copy and paste the above into a normal desktop launcher icon.
