It's infinity I have decided it has trouble with, sitting in my house in low light it's bang on every time. If I point it at trees some distance away it is a bit hit or miss.
Someone asked about shutter speed, usually a 1/1000th or less. When I shot film it was often 1/250th and 1/1000th being the quickest, no problem with vibration/shake then if that's what you are thinking.
Lenses most used 17-40mm, 50mm 1.4, 70 - 200mm f2.8. it happens with them all.
Those that don't have a problem, try it on infinity, I can see most people could go their whole lives and never focus on infinity unfortunately most of what I shoot is.
Kevin.
Haven't had a problem with it, and I do shoot fairly often with my 1Ds3 at or near infinity, but if you're doing aerial at those speeds, I do less that are infinity-and-wide-open, which would mask a lot of the focus errors you're seeing. I don't believe the problem you describe at all.
And if you're seeing the focus errors when you're shooting from the ground, then yeah, it's not the airplane (airplane?). I was suspicious of this at first, the Ds3's resolution is going to require a faster shutter speed for a sharp result than color film or your previous digital cameras would, but ... the trees-from-the-ground really nails this as a problem in your cameras AF.
In any case, if you have fairly consistent problems focusing on a fixed infinity target from the ground, you're using single-shot focus and you're getting feedback that AF thinks it's locked, that sure sounds like something to nail down and take up with Canon service.
Also, agree with Dwdallam that the physical focus mark isn't going to necessarily be right on your lens. In particular, at least with some lenses there's a detectable change in the offset over large swings in temperature, this is something I've observed playing with astrophotography.
--Joe