@relik:
I have successfully worked around this problem by adding irqpoll to my kernel 
parameters.

1. Add "irqpoll" to the line beginning with:
# defoptions=quiet...

2. Run:
sudo update-grub

3. Reboot

Since I added irqpoll, the two USB ports on my ThinkPad X61 remain
active.  I've used it for days with this setting, and suspended/resumed
many times. USB ports remain up.

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