ben,
One thing you might try first. Check your camera to see exactly where the focus sensors are. I discovered when using the center point focus, the sensor was really just barely in the indicator's upper left hand corner on my camera. A little more testing and I found they were all to the upper left of the focus indicators (which would make sense). Now, when I'm wanting the focus to be exact, I put the upper left hand corner of the indicator box dead on my target and that works. Yep, had the same back focus issue as you are. With a ........135L no less. All that to say, it could be the cam's indicators are just a little off or a small adjustment in your technique may be in order. I'll do anything to avoid shipping my stuff back to MawCanon.
~dp