Have you checked your BIOS settings? Maybe the USB ports were somehow disabled? Are you talking about the USB ports integrated into your motherboard, or some separate bundled USB card you have to connect to the motherboard?
Any updates Yakooza? Have you checked those BIOS settings? It's actually weird that the integrated ports don't work while the bundled ones do. I'm assuming there's something wrong with the connection between the rest of your mobo and your integrated USB ports.
That's why you don't buy Biostar. It could be that after a lot of use you managed to somehow mess up the physical connection to the motherboard. If you did you'll have to live with the extra expansion ports or get an ASUS board.