+1 to get this fixed! I just bought a 1T usb 3 drive and it has exactly the 
same failure to work in a USB 3 port, but works in USB 2. It is becoming hard 
to get external drives that are not USB 3, and they are getting less and less 
expensive, so the demand to make this work must be rising. I am running Xubuntu 
12.04 LTS on  a new MSI 970A-G46 motherboard so USB 3 compliance can be 
expected at the interface level, and a Western Digital external portable hard 
drive.
dave@britton:~$ uname -a
Linux britton 3.2.0-45-generic #70-Ubuntu SMP Wed May 29 20:12:06 UTC 2013 
x86_64 x86_64 x86_64 GNU/Linux

dave@britton:~$ lsusb -v -s 001:003

Bus 001 Device 003: ID 1058:1042 Western Digital Technologies, Inc. 
Couldn't open device, some information will be missing
Device Descriptor:
  bLength                18
  bDescriptorType         1
  bcdUSB               2.10
  bDeviceClass            0 (Defined at Interface level)
  bDeviceSubClass         0 
  bDeviceProtocol         0 
  bMaxPacketSize0        64
  idVendor           0x1058 Western Digital Technologies, Inc.
  idProduct          0x1042 
  bcdDevice           10.22
  iManufacturer           1 
  iProduct                2 
  iSerial                 5 
  bNumConfigurations      1
  Configuration Descriptor:
    bLength                 9
    bDescriptorType         2
    wTotalLength           32
    bNumInterfaces          1
    bConfigurationValue     1
    iConfiguration          4 
    bmAttributes         0x80
      (Bus Powered)
    MaxPower              500mA
    Interface Descriptor:
      bLength                 9
      bDescriptorType         4
      bInterfaceNumber        0
      bAlternateSetting       0
      bNumEndpoints           2
      bInterfaceClass         8 Mass Storage
      bInterfaceSubClass      6 SCSI
      bInterfaceProtocol     80 Bulk-Only
      iInterface              6 
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x81  EP 1 IN
        bmAttributes            2
          Transfer Type            Bulk
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0200  1x 512 bytes
        bInterval               0
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x02  EP 2 OUT
        bmAttributes            2
          Transfer Type            Bulk
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0200  1x 512 bytes
        bInterval               0

dmesg:
[76502.568148] usb 1-1: new high-speed USB device number 3 using ehci_hcd
[76502.702932] scsi7 : usb-storage 1-1:1.0
[76524.880212] usb 1-1: reset high-speed USB device number 3 using ehci_hcd
[76535.124043] usb 1-1: reset high-speed USB device number 3 using ehci_hcd
[76551.368092] usb 1-1: reset high-speed USB device number 3 using ehci_hcd
[76551.616151] usb 1-1: reset high-speed USB device number 3 using ehci_hcd
[76561.860043] usb 1-1: reset high-speed USB device number 3 using ehci_hcd
[76561.993705] scsi 7:0:0:0: Device offlined - not ready after error recovery

dave@britton:~$ lspci
00:00.0 Host bridge: Advanced Micro Devices [AMD] nee ATI RD890 PCI to PCI 
bridge (external gfx0 port B) (rev 02)
00:02.0 PCI bridge: Advanced Micro Devices [AMD] nee ATI RD890 PCI to PCI 
bridge (PCI express gpp port B)
00:11.0 SATA controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
SATA Controller [IDE mode] (rev 40)
00:12.0 USB controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
USB OHCI0 Controller
00:12.2 USB controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
USB EHCI Controller
00:13.0 USB controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
USB OHCI0 Controller
00:13.2 USB controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
USB EHCI Controller
00:14.0 SMBus: Advanced Micro Devices [AMD] nee ATI SBx00 SMBus Controller (rev 
42)
00:14.1 IDE interface: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
IDE Controller (rev 40)
00:14.2 Audio device: Advanced Micro Devices [AMD] nee ATI SBx00 Azalia (Intel 
HDA) (rev 40)
00:14.3 ISA bridge: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 LPC 
host controller (rev 40)
00:14.4 PCI bridge: Advanced Micro Devices [AMD] nee ATI SBx00 PCI to PCI 
Bridge (rev 40)
00:14.5 USB controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
USB OHCI2 Controller
00:15.0 PCI bridge: Advanced Micro Devices [AMD] nee ATI SB700/SB800/SB900 PCI 
to PCI bridge (PCIE port 0)
00:16.0 USB controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
USB OHCI0 Controller
00:16.2 USB controller: Advanced Micro Devices [AMD] nee ATI SB7x0/SB8x0/SB9x0 
USB EHCI Controller
00:18.0 Host bridge: Advanced Micro Devices [AMD] Family 15h Processor Function 0
00:18.1 Host bridge: Advanced Micro Devices [AMD] Family 15h Processor Function 
1
00:18.2 Host bridge: Advanced Micro Devices [AMD] Family 15h Processor Function 
2
00:18.3 Host bridge: Advanced Micro Devices [AMD] Family 15h Processor Function 
3
00:18.4 Host bridge: Advanced Micro Devices [AMD] Family 15h Processor Function 
4
00:18.5 Host bridge: Advanced Micro Devices [AMD] Family 15h Processor Function 
5
01:00.0 VGA compatible controller: NVIDIA Corporation GT218 [GeForce 210] (rev 
a2)
01:00.1 Audio device: NVIDIA Corporation High Definition Audio Controller (rev 
a1)
03:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd. RTL8111/8168B PCI 
Express Gigabit Ethernet controller (rev 06)

dmesg after uplugging from USB 3 and plugging into USB 2:

[78380.824151] usb 1-5: new high-speed USB device number 8 using ehci_hcd
[78380.959124] scsi12 : usb-storage 1-5:1.0
[78381.956823] scsi 12:0:0:0: Direct-Access     WD       Elements 1042    1022 
PQ: 0 ANSI: 6
[78381.957955] sd 12:0:0:0: Attached scsi generic sg3 type 0
[78381.963949] sd 12:0:0:0: [sdc] Spinning up disk.....ready
[78383.972835] sd 12:0:0:0: [sdc] 1953519616 512-byte logical blocks: (1.00 
TB/931 GiB)
[78383.973626] sd 12:0:0:0: [sdc] Write Protect is off
[78383.973635] sd 12:0:0:0: [sdc] Mode Sense: 47 00 10 08
[78383.974504] sd 12:0:0:0: [sdc] No Caching mode page present
[78383.974512] sd 12:0:0:0: [sdc] Assuming drive cache: write through
[78383.976875] sd 12:0:0:0: [sdc] No Caching mode page present
[78383.976883] sd 12:0:0:0: [sdc] Assuming drive cache: write through
[78383.986403]  sdc: sdc1
[78383.990004] sd 12:0:0:0: [sdc] No Caching mode page present
[78383.990011] sd 12:0:0:0: [sdc] Assuming drive cache: write through
[78383.990017] sd 12:0:0:0: [sdc] Attached SCSI disk

also  after attaching as USB 2:
dave@britton:~$ lsusb -v -s 001:008

Bus 001 Device 008: ID 1058:1042 Western Digital Technologies, Inc. 
Couldn't open device, some information will be missing
Device Descriptor:
  bLength                18
  bDescriptorType         1
  bcdUSB               2.10
  bDeviceClass            0 (Defined at Interface level)
  bDeviceSubClass         0 
  bDeviceProtocol         0 
  bMaxPacketSize0        64
  idVendor           0x1058 Western Digital Technologies, Inc.
  idProduct          0x1042 
  bcdDevice           10.22
  iManufacturer           1 
  iProduct                2 
  iSerial                 5 
  bNumConfigurations      1
  Configuration Descriptor:
    bLength                 9
    bDescriptorType         2
    wTotalLength           32
    bNumInterfaces          1
    bConfigurationValue     1
    iConfiguration          4 
    bmAttributes         0x80
      (Bus Powered)
    MaxPower              500mA
    Interface Descriptor:
      bLength                 9
      bDescriptorType         4
      bInterfaceNumber        0
      bAlternateSetting       0
      bNumEndpoints           2
      bInterfaceClass         8 Mass Storage
      bInterfaceSubClass      6 SCSI
      bInterfaceProtocol     80 Bulk-Only
      iInterface              6 
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x81  EP 1 IN
        bmAttributes            2
          Transfer Type            Bulk
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0200  1x 512 bytes
        bInterval               0
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x02  EP 2 OUT
        bmAttributes            2
          Transfer Type            Bulk
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0200  1x 512 bytes
        bInterval               0

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https://bugs.launchpad.net/bugs/1050352

Title:
  External USB 3.0 hard drive randomly disconnects and connects

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