Yesterday, I attended a Canon Demo day in Copenhagen and a fellow 5D3 photographer pointed out an issue to a Canon rep (and myself):
If you use:
* Back-Button Focus,
* AI Servo mode,
* Set the 'AI Servo 2nd image priority' to 'Focus', and
* Release the Back-button focus button for shooting,
The shooting speed will drop to ~3fps.
If the AI Servo 2nd image priority is set to 'Equal priority' or 'Shooting speed priority', the camera will "correctly" shoot at the full 6fps.
I put the correctly in quotes, because it is arguable whether this is the drop in fps is the expected/correct behavior or not. From a user perspective, we argued that since you've released the focus button, the camera should just shoot at the highest fps.