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Hi,
I found a workaround for Shortcuts for the Unity launcher because the Unity launcher shows wine instead of the actual opened program.
But I have no Idea how to insert this in the script.
As an example Microsoft Word 2010:

[Desktop Entry]
Encoding=UTF-8
Name=Microsoft Word 2010
Comment=PlayOnLinux
Type=Application
Exec=/usr/share/playonlinux/playonlinux --run "Microsoft Word 2010" %F
Icon=/home/nick/.PlayOnLinux//icones/full_size/Microsoft Word 2010
Name[fr_FR]=Microsoft Word 2010

You have to add this line

StartupWMClass=WINWORD.EXE

So:

[Desktop Entry]
Encoding=UTF-8
Name=Microsoft Word 2010
Comment=PlayOnLinux
Type=Application
Exec=/usr/share/playonlinux/playonlinux --run "Microsoft Word 2010" %F
Icon=/home/nick/.PlayOnLinux//icones/full_size/Microsoft Word 2010
StartupWMClass=WINWORD.EXE
Name[fr_FR]=Microsoft Word 2010

I don't know if you already know this problem but maybe I could help you to improve PlayOnLinux because I love it :D

It's fixed in development version, thanks to a patch contributed by Excalibr on IRC.