The last kernel running on this machine was:

Linux custard 3.0.0-15-generic #26-Ubuntu SMP Fri Jan 20 15:59:53 UTC
2012 i686 athlon i386 GNU/Linux

When shutdown this previous kernel correctly powers down the USB ports.
So, it looks like the quirk for the 590 chipset is still needed.  Is
there anything I can test for you?

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https://bugs.launchpad.net/bugs/936190

Title:
  nForce 590 USB power regression in 3.0.0-16

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