The software center places bad .desktop files in the launcher

When installing an application through the software center, it uses desktop files in /usr/share/app-install/desktop/ instead of /usr/share/applications/ resulting in applications that are not able to communicate with the launcher entries through the LauncherAPI

dbus-send --session --print-reply --reply-timeout=2000 --type=method_call --dest=org.ayatana.bamf /org/ayatana/bamf/matcher org.ayatana.bamf.matcher.RunningApplicationsDesktopFiles
method return sender=:1.60 -> dest=:1.232 reply_serial=2
   array [
      string "/usr/share/app-install/desktop/emesene:emesene.desktop"
      string "/usr/share/app-install/desktop/xchat:xchat.desktop"
      string "/usr/share/applications/firefox.desktop"
      string "/usr/share/applications/thunderbird.desktop"
   ]

In the above case xchat and emesene are affected.