The tool I would use for this is the "device manager" View "hidden devices" then move around to "View devices by connection" and trying to see which "Hub" it is going through. My system has only one "hub" that is not USB2 and it is not even on the computer itself.
Then you attempt to figure out which hub the different ports connect through, and even tag them if nessisary.
Again in the device manager, USB hub drivers in the "properties" "Advanced" tab of different hub types there can be interesting information in there , and the 2 switches to turn off telling you it was negotiated badly.
I have seen this occur (in XP) when the system is wrong about the port. I do not know what happens exactaly, some kind of misstep between the device and the driver and the system? I have corrected it before by removing, cleaning up the mess in the device manager, cleaning up the usb junk in devices, rebooting, and reinserting , back into the same port! and having it work?
It could also be effected if the motherboard chipset drivers were not proper or properly installed for the motherboard.
Possibility that the MS USB drivers were not correct/updated. It would not be to hard to check the USB driver items, and see if they corelate with another properly updated machines driver versions.
Rare possibility that it could be effected by some setting in the motherboard BIOS, for the usb items, one of the lowest level locations.