I have similar behavior.  I am on 11.10, and have seen this for a couple
of years (certainly 10.04, maybe 9.04).  For me it is a keyboard and
mouse plugged into my ThinkPad docking station that die.  If I plug them
into my laptop's ports, they work fine.  I also occasionally have my
laptop's keyboard and trackpoint die in the same way, in which case I
have to reboot.  All works fine after reboot, at least for a while.
Like the OP, it's random and hard to reproduce.  Unlike the OP, I've
never once had it start working again.  lsusb -v segfaults when this
happens:

# lsusb -v

Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Couldn't open device, some information will be missing
Device Descriptor:
  bLength                18
  bDescriptorType         1
  bcdUSB               2.00
  bDeviceClass            9 Hub
  bDeviceSubClass         0 Unused
  bDeviceProtocol         0 Full speed (or root) hub
  bMaxPacketSize0        64
  idVendor           0x1d6b Linux Foundation
  idProduct          0x0002 2.0 root hub
  bcdDevice            3.00
  iManufacturer           3 
  iProduct                2 
  iSerial                 1 
  bNumConfigurations      1
Segmentation fault

Note the warning after the first line of text.  Sadly, it doesn't say
which device it is looking for.

When this happens, there is a light on the lid that turns on.  It has a
square with three dots in a triangle shape in it.  That light never
lights for any other reason.

Currently the audio port on the laptop (but not the ports on the dock)
do not work, speakers do work, and the camera does not work.  I suspect
this is because of the USB problem.  Generally they work fine.

Finally, I am on a ThinkPad W510, and was on a T61 before this with the
same problem.

Linux glup 3.0.0-26-generic #42-Ubuntu SMP Wed Sep 5 08:37:08 UTC 2012
x86_64 x86_64 x86_64 GNU/Linux

Ubuntu 3.0.0-26.42-generic 3.0.42

Note that this is both a mouse and a keyboard, and now maybe other
devices, but not flash drives.  The same devices work ok in different
USB ports, but it's less convenient if the dock ports don't work and
really bad if the camera and audio stop working.

It's happened with different keyboards and mice.

Thanks,

--jh--


** Attachment added: "lspci-vvnn"
   
https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/1016267/+attachment/3373363/+files/lspci-vvnn

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https://bugs.launchpad.net/bugs/1016267

Title:
  0458:003a USB mouse stops working after unplug/replug

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