I have had the same issue on occasion with my D300S in low light situations. It is very frustrating because most times you lose the shot/moment. When I have the issue, the only thing that seems to correct it is to point the camera at a brighter area and then depress the shutter. Sometimes after I do that I can go back and take the original photo with no problems.
I'm not sure if it is the sensor having trouble reading the focus or not being able to get proper readings for setting internal variables. But the problem you describe is exactly what happens. It seems this has happened mostly with my zooms (12-24; 28-70; 70-200).