Have you guys MFA'ed the lenses? I know you can't on the 60D but on other bodies you can. But the reasons are actually quite simple. All hardware has some level of slop. They are designed for perfection but during manufacturer anything that comes in some range, say 5% of perfect is considered fine. If you have a body and lens with are perfect, all is well. If you have a body that is on the +5% side and a lens on the +5% side, all might still be well. But if your bode is on the +5% side and the lens on the -5% side, it may be far enough off to notice it.
I had that experience with my 100-400 and 40D. It was so bad that I was redy to dump all my Canon equipment and switch. Both the body and lens made multiple trips back to Canon and they just couldn't get it acceptable.
But I got a good deal on a new 50D with MFA and was able to calibrate the lens to the body. The results were very noticeable. It turned a piece of junk 100-400 into one of my sharpest lens. Below is a sample test pic I took. The left is the lens with no adjustment and the right with adjustment applied.
