I've had similar problems with both 7D and 5DMII... I suspect the problem is AF mode, single point, manually selected, with expansion points (which is what the mode with the surrounding micro points showing is called)... in all the cases it's the mode I was using.
Weird thing with 7D in particular was that reviewing the images later in DPP it showed the center point being used, and dead on the subject, but still the image was grossly misfocused a lot of the time. I had better luck with my 50D (which don't have expansion points, so I was only using the center point... and about the only time focus would be grossly off was when the user - moi - let the AF point drift off the subject during movement).
With 7D only, I also shot a test series "in real life" using all AF point mode... Even though DPP shows one or more points lit up right on the subjects... sometimes focus would be dead on, other times it was off a little, sometimes a lot, and still other times it missed by a mile. Focus would be on points that weren't even lit.
With 50D I rarely had focus issues that I didn't blame on myself. Most often it was too shallow depth of field combined with where I chose to place the AF point. I can hit probably better than 90% in focus with 50D, even in the same locations with the same, tough lighting situations. Haven't been nearly as successful with 7D or 5DII so far.
All the testing I did was using AI Servo and "thumb focusing". One of the most extensive sessions with 7D was a very cold one day (for N. California) and after about 6 hours shooting I'm sure there were times I simply cued AF too late or missed it entirely. Wearing gloves some of the time didn't help either!
But, essentially I'm going back to using single point on both 7D and 5DII now... That will mean center point most of the time on the 5DII, since it's only got that one cross sensor type. With 7D might be able to use some of the other 18 points more freely. We'll see.