Try it with Live View on a tripod and manual focus at 10x magnification with some static object with texture. If the result is razor sharp, you know it's an autofocus issue that could possibly be resolved with microfocus adjustment. That was the case with my 400 f2.8, where it was backfocusing a little too much for my liking. Now it seems to be right on the money.
Cameras: 1DX, 1D4, 20D, 10D, S90, G2
Lenses: Canon 10-22mm, 16-35mm f2.8L II, 24-70mm f2.8L, 70-200mm f2.8L IS, 300mm f2.8L IS, 200mm f2L IS, 50mm f1.4, 50mm f1.2L, 85mm f1.2L, 1.4x TC, 2x TC, 500D macro, Zeiss 21mm
Lighting: 580EX, Elinchrom 600 RX's, D-Lite 4's, ABR800, 74" Eli Octa, 100cm/70cm DOs, Photoflex Medium Octa and reflectors, PW's, Lastolite Hilite, Newton Di400CR bracket