I have the same (type of) error on a T61 with kernel 2.6.22-14-generic.
The single USB Port on the right works all the time. The two USB-Ports on the 
left sometimes don't work. I couldn't figure out any regularity, when the ports 
get disabled. 
However, when I reload the kernel module for USB with 'sudo modprobe -r --force 
ehci-hcd' the USB ports work again, also for a longer period than 10 min. (thx 
to Nemanja Stefanovic tip!)

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kernel disables irq after 10 minutes
https://bugs.launchpad.net/bugs/126369
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