There's no need to disable the onboard USB ports.
What we have here is the classic ALi USB card problems. They are unreliable. If you search the forums, you will find many people who had ALi card problems.
You must do what they did - exchange the card for an NEC version. Adaptec, ADS, Belkin, D-Link, Keyspan, Koutech and Siig all make NEC cards.