> Pink Ink, thank you for reporting this and helping make Ubuntu better.

You're welcome :-)

> Could you please plug your external SATA HDD into a USB 2.0 port,
unplug all other USB devices...

The problem is that I cannot unplug ALL other USB devices, because I need at 
least my USB keyboard to execute the command.
I hope it helps also with the keyboard plugged in:
USB 2.0 port:
$ lsusb
Bus 003 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 002 Device 004: ID 174c:5106 ASMedia Technology Inc. 
Bus 002 Device 003: ID 05af:0408 Jing-Mold Enterprise Co., Ltd 
Bus 002 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 001 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub

USB 3.0 port (to be complete)
$ lsusb
Bus 003 Device 002: ID 174c:5106 ASMedia Technology Inc. 
Bus 003 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 002 Device 003: ID 05af:0408 Jing-Mold Enterprise Co., Ltd 
Bus 002 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 001 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub

The HDD case is this one: ID 174c:5106 ASMedia Technology Inc.

$ dmesg   (with USB3.0)
...
[    8.519581] EXT4-fs (sda2): re-mounted. Opts: errors=remount-ro,commit=0
[    8.521508] EXT4-fs (sdb1): re-mounted. Opts: errors=remount-ro,commit=0
[  442.166345] usb 3-3: new SuperSpeed USB device using xhci_hcd and address 2
[  447.186949] usb 3-3: unable to read config index 0 descriptor/start: -110
[  447.186955] usb 3-3: chopping to 0 config(s)
[  447.187717] xhci_hcd 0000:03:00.0: WARN: short transfer on control ep
[  447.188965] xhci_hcd 0000:03:00.0: WARN: short transfer on control ep
[  447.190217] xhci_hcd 0000:03:00.0: WARN: short transfer on control ep
[  447.196906] xhci_hcd 0000:03:00.0: WARN: short transfer on control ep
[  447.197327] usb 3-3: no configuration chosen from 0 choices

Question about upstream kernel testing:
I'm not sure which one to take. What do you mean by "the one all the way at the 
bottom"? bottom of which directory?
The daily current seems to be the same as the latest for natty...
http://kernel.ubuntu.com/~kernel-ppa/mainline/daily/current/linux-image-2.6.39-020639rc4-generic_2.6.39-020639rc4.201104191410_amd64.deb
Would this be a right one?

(I'll call it a day now - I'll come back on this issue, testing the
kernel these days)

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https://bugs.launchpad.net/bugs/1031982

Title:
  USB 3.0 port does not work with external hard disk

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