It's possible that you're experiencing front focus or back focus issues. Simply put, this means that your camera and lens habitually focus in front of or behind what you think you're focusing on.
There are tolerances in manufacturing both cameras and lenses. Sometimes when both are at the edge of the tolerance range (or the lens is not within the manufacturer's tolerances), it results in front focus or back focus.
You can test for this yourself and correct the problem (well, kinda) using something like LensAlign Pro, invented by the same guy who came up with WhiBal.
LensAlign Pro (I believe the current version is LenAlign Pro II, which costs less than the original model) will let you diagnose the problem. Then you can make an adjustment in your camera that applies only when the lens in question is mounted on your camera.
I say kinda because, in the end, you'll have focus optimized for a particular focal length and distance with your zoom lens. This is even more true if the lens was not manufactured to the specified tolerances.
One alternative is to send *both* the camera and lens to the manufacturer and let them adjust both. Still, from what I've read, you're not likely to end up with what you'd have with an optimal camera and lens. (Don't ask me why.)
A better alternative, if your lens is still in warranty, is to exchange it.
Last year I bought a used 28-105mm f/3.5-4.5D Nikkor for use when I didn't want to tote both the 35-70mm f/2.8 and 70-200mm f/2.8 lenses. Turned out the 28-105mm has a severe front focus issue. In my case, the solution turned out to be leaving the lens in the closet when I shoot.