Keep in mind that it's not terribly uncommon for a certain lens/body combination to need a microfocus adjustment (that's why the option is included on newer cameras). I have a 70-200 f/2.8 L IS that requires a heavy MF adjustment on my 50D, yet no adjustment is required on my 7D.
When you set up a controlled test, make sure to do it at 100 ISO--you don't want noise (and itsautomatic removal) to skew your sharpness results.