Update: this note apparently hit a nerve, with many peeved readers emailing to describe similar experiences with their 5D Mark II bodies. I don’t have any immediate answer, but my one suggestion is to prefer the central focus point and use “focus lock and recompose”, which isn’t perfect but often works better than using an off-center sensor.
With my D3x away for service, I pressed the Canon EOS 5D Mark II into duty shooting a children’s orchestral group with the EF 85/1.2L II. In the past I’ve shot such things with the Canon EOS 1Ds Mark III, a pro body, and I’ve never had focusing problems.
But with the Canon 5D Mark II, it was a joke— most of the photos were ruined by backfocus. I really couldn’t believe what I was seeing; I put the focus sensor squarely on a good contrast area, and the 5DM2 screwed it up repeatedly. I had to compensate by focusing a little more forward. I’m not sure what’s going on there, but I’m just going to stick to the 1Ds Mark III for such things.