Comment 4 for bug 551748

I have this with almost every app I pin to the dock.

Per suggestions above, I tried the following to pin apps to the dock:

1) Start from app menu or terminal
2) Right-click the dock icon, and pin it to the dock

Starting another instance right away results in proper grouping (no duplication). BUT, as soon as I close all the windows, and then launch another instance (i.e. with gnome-terminal), then a duplicate icon appears on the right, and all new app instances are grouped under it.

Checking in gconf reveals that the items in the dock are correctly pointing to the /usr/share/applications launchers, but this problem persists. This happens even with many single-instance apps (like rhythmbox), although some (like empathy) behave correctly. It's very inconsistent.