I've recently encountered a problem where if I lock GNOME Terminal and/or Byobu to the Unity launcher, then close and restart it, a second icon of the same application would appear in the launcher. The launcher would keep producing a duplicate icon for every subsequent re-launch of the application. Needless to say this is extremely annoying but fortunately I've found a workaround. It turns out the two ways to put an icon in the launcher - locking and dragging from the Dash behave differently.
Normally I would:
So if you find yourself hitting this issue - remove the icons you've created using "The wrong way" and use "The right" one.