Apps appearing "open" in the dock that are not

I have noticed that after upgrading to Mountain Lion, exactly two apps appear permanently "open" in the Dock (glowing dot) while in fact they are not open. This only happens with two apps at the moment: Skype and Billings by Marketcircle.
Precisely, if I leave any of two apps open before a restart and mark the corresponding dialogue to open all windows anew, Skype and Billings will not open but will show as open in the Dock. A double click then regularly launches the app.
Has anyone seen this?

You say they are open but in fact they are not.  It is true they are not Open, Open but they are active!  If you do not want apps to be "Active' at login you must quit app before shutdown, if you do not ever want any apps to be "Active" at login then do this as shown here....

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