Clean the lens contacts and lens mount. If that doesn't fix it then send the camera in for repair.
My D3S stopped focusing. I cleaned the contacts and everything I could think of doing. It got worse over a 2 month period. It seemed to be the body so I sent it back to Nikon. The D700 had no issues so I decided it was probably the body. Nikon replaced the lens coupler and life is good. The D2S has worked perfectly ever since.
My 'black' frames were shot with auto exposure - aperture priorty. The camera used 1/8,000 second. The sensor picked up very bright highlights so I knew the sensor wasn't at fault. Cleaning the lens mount often works but not in this case.