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I have a problem with my external HDD (WD My Book Essential 1TB) working on USB 3.0 port.

I'm using dual boot setup with Windows 7 and Ubuntu 11.10, both 64 bit.

While I'm running Windows and rebooting back to Windows everything works well. When I'm switching to Ubuntu everything works great as well. But after the first reboot from Ubuntu, neither Windows nor Ubuntu mounts the external drive. I have to reboot the device manually. I suspect that the problem is with unmounting the device on shutdown in Ubuntu.

This only happens with USB 3.0 ports. When I plug the same device into USB 2 port the problem doesn't persist.

Does anyone have the same problem, or a clue what might going wrong?

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I had a similar problem. My Seagate USB3.0 drive was not being recognized at the boot time (neither Windows7 nor Ubuntu). I added a line with the word usb_storage in /etc/modules and it is now being recognized by Ubuntu.

However, Windows7 still has problem recognized it at boot time. I hope someone has a solution for that.

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Questions about Windows 7 should be asked on Super User. You might consider asking there about the Windows half of the problem. –  Seth Dec 27 '12 at 21:02
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