I have a SAN administration tool I use that launches a Java app. The desktop shortcut that runs it looks like this:
When I pin this shortcut to the taskbar and launch it, I get a second instance of the icon in the taskbar (shown as running), and the pinned icon never changes to a "running" icon. If I launch another instance of the app (Shift-Click the non-running pinned icon) it will pair up both running instances and show me both when I hover over the running icon, so that part works, but it appears that the mechanism that links a running app to the taskbar gets confused by the shortcut.
Bug, feature, something worth reporting?