Now, if you, for a moment, has so much as an ounce of doubt with your Nikon D90 focus engine integrity, I would first advice you to read up this guy's two-cent worth of explanation (I think its much more than that) and perform the simple test yourself [here].
If not, just send it in and the Nikon technician will confirm this with their set of tools. Tim Jackson sure shed some light with regard to this problem I sometimes face with the Nikon D90.