I would definately set the aperture to 5.6-7 just to see if it makes a difference. Try a couple of shots on manual and a couple on auto and see if that helps you narrow it down.
It could be a backfocus problem but that seems to be thrown out there so much these days, that I'm starting to believe it's not near as common as most people want to believe it is.
You are overiding your AF point and setting it manually, right? I think you said you were. I have long since given up on letting my Canons pick my AF point for me. I can't tell you how many shots I missed and how frustrated I was with my cameras before I finally learned that the camera just wasn't as good at deciding what I wanted to focus on as I was!
If you're fortunate enough to have a lens that supports constant manual focus, you can set auto-focus to a point and let the camera
get it close quickly and then tack it in manually just before you shoot. This is what I do most of the time.
Another good test is the battery test.
1) Get 3-5 batteries. D's work best, IMO but any size can work.
2) Stand them up 1 after the other from front to back on a table-top, 2 inches apart, and half sticking out from the one before it when viewed from the front. Staggered, in other words.
3) Set your aperture to various settings from open to more closed
4) Take a shot, preferrably level with the table, focused on each battery from front to back, document your settings for the shot, and review your results
I've probably taken a few hundred shots doing this at various apertures and shutter speeds. I've probably learned more about my cameras and how they behave by doing this, than any other single thing I've ever done, and it all started out as a focusing excercise. Now I do it just to teach myself things. The batteries don't complain while I'm learning!