Hello maxcham, welcome to Windows 7 Forums.
I have a 2, 3rd party apps that do the same thing, nothing to worry about, the 2nd icon just shows that the program is open and running.
You could unpin it, then open the program from "All Programs", then right click the icon in the "Taskbar" and pin it, then close the app and re-open it using the newly pinned icon. See if that changes it, I kind of doubt it, but it's worth a shot and like I said, it's nothing to worry about.
Hope this helps,
Don