At first I thought my issues were only related to the central point as well since for birds and wildlife that's the only point I use. So I have my C1 setting setup for wildlife "portraits", central spot, Av, AF settings for erratic subjects (can't remember the exact one off the top of my head), one shot and other specific things set. My C2 setting was for BIF so I used all AF points (flexi zone I think), Tv and AI Servo. Those shots were often not in focus either. Now, when I say not in focus, some were very obvious but others I couldn't tell until I got home and could see how soft they were. At 1/2000 or faster for BIF, I should get most if not all sharp so that also told me something was wrong with the overall focusing system. I would then take my 6D and set things as close as I could to my 7D settings (obviously the AF is WAY different) settings and shoot. Nice and sharp most of the time.
Obviously your mileage may vary but if you have any doubts, the shipping costs back to Canon to have them look at it is small in comparison to how much money and effort you've already spent fussing with it.