In short it’s because the BIOS routes IRQ lines incorrectly in IO-APIC mode. Disable IO-APIC mode if you want to use the onboard USB on a PR440FX motherboard.
See the following links.
http://www.mail-archive.com/linux-usb-users@lists.sourceforge.net/msg00850.html
http://forums.2cpu.com/showthread.php?threadid=6697
http://lists.freebsd.org/pipermail/freebsd-current/2005-October/057441.html