I'm at work, so I didn't bring my pcmcia and external usb stuff... so I don't know if this'll work, but it looks promising.

I had a squiz at linux-usb.org/usb2.html, and it says that before the 2.5.something kernels, you had ("have") to manually remove certain modules in order for the shutdown to effectuate cleanly. I can't try this until this evening or maybe this weekend, but it says to do this - as root, of course -

rmmod ehci-hcd
rmmod ohci-hcd
(then shutdown)

Or you can upgrade to something past 2.5.29. Maybe you could remove other modules related to usb, like usb-uhci or even usbcore. Heck, i'd try it.

I'll look forward to trying it out myself..

dana