Hey my friends computer is way old and when it had windows 98 on it it wouldn't shut down. It would reach the screen that says that windows is shutting down but it never reaches the screen that says it is now safe to turn off your computer. I know that microsoft has acknowledged the problem that windows 98 may not be able to shut down all network connections and has sent out a patch for this but now that we clean installed windows xp pro on his computer it is still doing the same thing, is the bios set incorrectly, what do i change?

His computer most likely isn't ACPI compliant and therefore the OS can't control the power settings like it can a newer computer. You can check this by looking at what kind of power driver is installed on the machine in Device Manager, under the Computer branch.