In my case, a BIOS upgrade solved the problem.

For anyone else desparately googling for this problem: 
it's a Dell Dimension C521 with an nVidia card, and I upgraded the BIOS from 
1.0.3 to 1.1.1. 
Changing kernels, disabling nvidia-driver, removing xorg-driver-synaptic and 
various other attempts at solving it did not make any difference, but the BIOS 
upgrade seems to have done the trick.

-- 
USB stops working after a while
https://bugs.launchpad.net/bugs/228746
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