I have the same problem on my ThinkPad R61 with Gutsy, generic kernel. I 
updated the BIOS, changed the IRQ's from 11 to auto, but unfortunately nothing 
has changed.
There is 3 USB, 1 on the left side 2 on the right side of the notebook. The USB 
on the left side is working always but the 2 others are gets disabled. I use an 
usb mouse, which works properly, after the kernel message too, but when I plug 
out then plug in it doesn't.

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