2.6.39-3? Do you mean the mainline 2.6.39-oneiric kernel?

Your best best is to go back to 2.6.38-8-generic, where USB3 works, or
to compile your own 2.6.39 kernel but with commit
dfa49c4ad120a784ef1ff0717168aa79f55a483a reverted. I've attached this
particular commit in case it helps.

** Attachment added: "commit that _breaks_ USB3"
   
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/779826/+attachment/2142339/+files/usb3fix

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https://bugs.launchpad.net/bugs/779826

Title:
  USB3 devices stopped working after kernel upgrade.

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