I have the same problem with 2 out of the 3 USB ports on my HP Compaq C714NR. It seems that it physically has 2 bad USB ports. I usually build and service my own computers, but laptops I usually have serviced unless it is hard drive or memory change. The guys at Geek Squad from Best Buy said the USB controller on my board was faulty. We already tried fresh installs of Windows and updating the BIOS. Nothing seemed to help it. They said I need to replace the board, and that happens to cost $50 more that what the laptop cost when it was new... like $600. Your laptop is similar to mine (but a higher grade), if a fresh install or recovery of Windows doesn't fix it, then it is likely you've got failing USB ports.
BTW, I've has this problem on 2 HP laptops. Never on any other laptop I've owned like Dell or Acer.
Are these the front panel USB ports or the back panel USB ports on the motherboard?
You can check the connector cables on the case front panel ports and see if the connection to the motherboard USB ports might have come loose, either on the case end or the motherboard end.
The HP Pavilion 9000 is a laptop. This advice does not apply. Dead USB ports on laptops can be a pain that usually can only be resolved by the manufacturer, unless you are a repair man or if it is software related.