I believe it followed the 747 crash off the US coast a while back and a ground explosion in a 747 centre tank. The implication/diagnosis was that the pumps had overheated or wiring had shorted causing the problems, so it was arranged to turn them off as a 'normal' procedure while they still had fuel coverage in the tanks. They can of course, be run to empty if the fuel situation requires it and the scavenge system normally takes care of using up the remaining fuel.
As I understand it the 'fix' involves modified pumps.