Have you tried resetting the camera? I've had my D90 go wonky after fiddling with the settings. One dumb question, have you checked your exposure comp settings?
Have you reset the camera to factory defaults? Would be worth trying.
You could also take a photo in Auto or Program mode noting what the Aperture is being set to then take the same photo in Aperture priority mode and compare the Exif data to see where the settings are different.
I do not know anything about the D90 but I would go through all your sub setting manually. On my camera auto reset does not reset all the changes I made to my camera. Also check any new filters installed on the camera.