I experience this problem as well. I added launchers to the Unity bar by
opening all applications menu and dragging their icons to the Unity bar
and dropping them there. Once I used them to launch the applications
there was no triangle indicator showing the application running. My post
to the Ubuntu forum is http://ubuntuforums.org/showthread.php?t=1812036
and there is a screenshot showing Chromium open but no indicator that it
is in use on the Unity bar. I will try removing that launcher, launching
Chromium from "applications" and then right click and select "keep in
launcher" as was advised by another user on the forum. However, this
behavior should remain consistent no matter how the launcher is added to
the Unity bar.

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https://bugs.launchpad.net/bugs/772063

Title:
  App icon on the Unity Launcher lost track of running instance

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