Someone posted a new Canon published Mark III guide on one of the forums that talked about how different AF CF settings work, particularly for different scenarios. It is available here... http://www.pbase.com/photo3nz/mark3
and the pages can be saved for printing.
The one thing that stands out to me, is the way Focus Priority works vs. how I thought it worked. I thought that Focus Priority would not take a shot if it wasn't focus locked. According to this guide, that is not true. It says that ...
1st shot:
With AF priority (C.Fn III-3-0 or C.Fn III-3-1), a fixed period of time is allotted for focusing (the lens-driving time). Focus does not need to be achieved to take the shot, but with more time to achieve focus, priority is given to achieving focus. With Shutter release priority (C.Fn III-3-2), pressing the shutter button completely will take the shot even during focusing.
This explains why you can still get OOF shots in Focus Priority.
I'm starting to think that since I'm the only one that doesn't have a perfectly focussing IIN. 
