Roger, I had that same problem and called and complained. A supervisor comped me with a 1000 mile "good will" award to make up for the lost miles which were less than what she gave to me. Call and make sure that you speak to a supervisor when you make your case.
Originally posted by Roger:
Be careful not to expect status mileage bonus credit for flights BETWEEN achieving status and the Saturday night update. You won't get it!
In my case, it's only 125 miles minimum bonus that I have 'lost'. If it had been a Transatlantic or Transpacific, I would be very angry indeed!