unity-panel apps running in the background

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http://askubuntu.com – i noticed that some of my apps are in the background in unity-panel. the apps are vmware-workstation,jupiter, empathy this is what i mean as you can see on the left some of my apps are running but in the background if i didn't set my unity-panel to see-through i wouldn't have noticed it. if i restart my laptop and start empathy it doesn't go in the background and also when i run compiz --replace the apps are back in the foreground this happens a lot when i am working my apps are suddenly in the unity-panel background? (HowTos)