System shut down issues

I am working on an issue for friend on an HP Pavilion 6553. When windows shutsdown the system the green power LED dims down by 50% and the power supply fan slows down but doesn’t stop. If hit the power button the system boots up like noraml runs through the hardware checks and then loads windows just fine. But I can’t figure out how to get a complete shutdown. The problem persists no matter whether it has Windows XP or 98SE. Someone had installed XP on the system with all the extra XP junk and the system just didn’t have enough power to run that O/S very well so I wiped (FDISK & FORMAT) the hard drive and installed 98SE.