Originally posted by fwbigd Sound like the lens might be decentered
Yup, agreed.
If you switch into live-view, zoom in all the way, and manually-focus on a flat target, can you get everything sharp? If so: AF problem. If everything is always soft (or some areas of the image are soft), you've got an optical problem with the lens (the most common is decentering). This has nothing to do with the AF system.
Either way, I'd either exchange it, or send it in under warranty.
AF tuning is a cute trick that I use on old AF primes and lenses that aren't under warranty anymore; however, if I buy a $1000+ brand new lens from an authorized dealer, and it doesn't work perfectly, it's going back.