A OS can disable a USB port because it draws too much current. This problem once drove me crazy on a dual-boot machine because one OS had no problem with the devices I was connecting through a hub to a single port, whereas the other OS silently objected to the current level in that port and disabled it. So if you're using a hub, try disconnecting devices from it. BTW, in my dual boot set-up, one OS recognizes ALL the USB ports, but the other OS recognizes only SOME of them: grrr!
I don't know if this is relevant but it might be. We got new computers at work once, and after a couple of months the floppy drives began to fail. Boss was getting replacement drives left and right. Real problem? Nothing to do with the drives: the batteries were cheap and funky; erratic battery performance screwed up BIOS settings, and the machines couldn't recognize the drives. For a month or so, while I waited for my new battery, I spent 3 or 4 minutes a day resetting the 9066@## BIOS
Just found this one in the googles: "In XP, after a USB port isn't used for a long while the USB driver built into the OS sets the OHCI controller to suspend. When you plug a device back in, it can sometimes fail to 'wake up' properly. This problem was supposedly fixed in SP1 but there is a related registry hack that may still be able to help"
http://www.ntcompatible.com/Desperately_need_help_---_USB_Devices_Not_Recognized_t32356.html