http://bugs.winehq.org/show_bug.cgi?id=51230
--- Comment #15 from Zdeněk Kopřivík zdenek.koprivik@post.cz --- Hello, I've just came here to create a bug report for per application "virtual desktop" option being broken, if the application is started via "wine start", but it seems you already know.
In my case: wine Empires.exe -> launch Age of Empires in VD as expected wine start Empires.exe -> launch AoE without the VD -> broken
You wanted a real world use case for a mixed VD settings, so here you are:
I'm using system wide WINEPREFIX to launch most of my old games and some network management tools, mostly running the executables directly from Dolphin (which is using the "wine start" command). For old games without native "window mode" support and also without native FullHD resolution support, you'll get a black screen and a small rectangle with the game in the top left corner, because the game is not allowed to switch to its fullscreen resolution on wayland. So, for such games it is prefferable to use the VD to simulate windowed mode, but for the rest of my apps I prefer the default setting without VD.
Until recently I've been using the same setup on my old PC with Wine 1.6 without any issues. Now I've upgraded the PC and updated my system and the same setting doesn't work anymore.