Comment 13 for bug 665819

I was having the same problem with several of my wine apps and I finally fixed it! You need to reformat the .desktop entries for the relevant program in /.local/share/applications and /.local/share/applications/.wine/[etc...]. For whatever reason wine doesn't correctly format the .desktop links for most files and also has a tendency to start files through start.exe and windows .lnk. To fix this, you need to specify the path the to the executable separately from its exec entry. For example:

[Desktop Entry]
Name=World of Warcraft
Exec=padsp wine WoW.exe -opengl
Path=/home/patrik/.wine/dosdevices/e:/Games/World of Warcraft
Icon=/home/patrik/Pictures/wow.svg
Type=Application
StartupNotify=true
StartupWMClass=Wine

#change the e:/ in path to whatever drive your application is on according to wine