I'm seeing this as well. My example app, that I'd like to sort out, is
Picasa. I've added a StartupWMClass=Wine entry to the .desktop file I'm
using to launch Picasa from the Unity Launcher, but it still doesn't
match the resulting running Wine app. I wonder whether the solution that
Docky implemented (see bug #596092) would help here?

In the case of Picasa, it actually bundles its own Wine runtime and
xprop shows WM_CLASS of "Picasa3.exe" "Wine" - and the running binary is
called Picasa3.exe

Integration of Wine apps in Unity is not great at the moment and it's
fairly clear that the Wine folks are unlikely to make special efforts to
help on the Unity side (see e.g.
http://forum.winehq.org/viewtopic.php?p=60406) so the more that can be
done in Ubuntu / Unity itself, the better. Little things like icon /
window / application matching for the Launcher would go a long way as a
starting point.

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https://bugs.launchpad.net/bugs/702452

Title:
  [launcher] Wine applications are wrongly matched

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