I had a similar problem after receiving mine. After going through extensive testing, I felt it had to be a problem with the lens itself so I sent it to Canon in late April. It was returned a week later, and the difference was phenomenal. I'm finally getting the results I should have gotten in the first place: very sharp images and a significant increase in the number of keepers.
According to Canon, "It was found that the adjustment of the circuit board was incorrect causing inaccurate auto focus."
Before the adjustment, I was getting about 10 percent keepers. Now, I'm getting about 70 percent. The 30 percent I end up deleting are mostly repeats and/or poor technique (excitement causing vibration) with probably 30 percent of those due to an actual miss in focus. This is probably more in line with how the lens should perform.
It is possible you got the same initial guy that adjusted the circuit board on my lens.
Wade