All of my lens are auto focus. They all have 5 contact points on the lens. The info sheets that came with these lens say AF AIS. When I was updating my equipment I kept these lens because they were made in Japan, and I take great care of my gear. I have a 105 2.8D macro and a 28-200 3.5-5.6D in this group. As I said they all worked auto focus on my D300 and I had a D70s that they all worked on. My latest purchase was a 300mm F4 ED and a 18-105 DX which all work great. Maybe the tolerance on the D90 is a little on the tight side, and of course I don't want to force the lens on to the camera body and demage it.
The only answer I have at this point is to update some of these lens for newer lens.