hmmm, this is an interesting problem. i've seen odd usb problems before. you know one strange thing i've encountered is the usb controllers, after you use several different usb sticks, usb external drives, and usb external dvd/cd drives, and usb gadgets, that the hub gets all these things installed on itself, and becomes confused between them all for some strange reason.
If it's just a shortage internal to the usb port, that's obviously different and at once noticable, as it causes a short that wont let the pc boot. I've rarely seen loose usb data connectors soldered to the motherboard... Usually someone tries to plug something in without first looking to see which way the usb port is oriented, and they jam it in there mashing the plastic thing against the metal of the case shorting it all out.
but yah i'd be interested in knowing the resolution of this issue, do keep in mind that some systems won't boot if something is plugged into a usb port, b/c it tries to boot from that instead. One simple trick, is to get nirsofts freeware usbdeview program, and look at all the things gunked up on your controllers. Then just delete a bunch of it that is not in use and safe to remove, oddly, this fixes the strangest problems one might encounter.
Finally I advocate getting a usb port hub that is powered, and plugging that sucker via long wire into the usb port on back of the pc, and doing all your work in the front, this way you are not always blindly plugging stuff into a tiny hole the wrong way in an effort to be fast, and not bothered by turning a box around and all the attached usually too short or tangled cables.
