At seemingly random points during normal computer usage, my usb completely stops working.
I would suspect that the cause is a faulty piece of hardware. Something sending the wrong signals can bugger up some USB buses, as i've experienced many times trying to develop an in-house USB device for laptops.
Maybe try a different mouse for a while (also USB - there are some really cheap ones out there), and see if it still happens.
I know it worked before 2.6, but 2.6 may be enabling higher bandwidth or some other such change that could involve more power going through the bus.
HTH
MAL
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