I believe I may have found a bug in ObjectDock (at least under Vista, cannot say about XP).
If the box to Load ObjectDock at Startup is checked there are two instances of ObjectDock running after a reboot or restart. This is verifiable via TaskMgr.
If that box is not checked there are none.
If that box is not checked, but a shortcut is manually placed into the user's StartUp folder, there is only one running.
It appears that checking that box causes an shortcut to be created in the user's StartUp folder and automatically starts ObjectDock. Unchecking the box also removes the entry in the user's StartUp folder.
Therefore, the work-around is to not check the box, but manually place the shortcut into your StartUp folder.