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I have a 3TB Seagate Backup Plus Desktop USB 3.0 drive, which works fine when in its enclosure, but when I get it off its enclosure and directly plug it as an internal SATA drive, it's just not properly recognized (it works again when used in the enclosure).
My systems’s motherboard is an ASUS P8P67 LE, which has two SATA 6.0 Gb/s and four SATA 3.0 Gb/s ports.

When used as an internal SATA drive Windows 7 asks if I want to format the drive, as if it didn’t have a proper filesystem, and if I use the DISKMGMT.MSC tool (typing that in the start menu) I get completely wrong information about the drive.

It says the drive has 3 partitions (349,31GB of RAW data and two unassigned partitions of 1698,68GB and 746,52GB). This information is plain wrong, since the drive, when used in the USB enclosure, works as a single NTFS partition (2794,52GB). How come it’s shown as 3 partitions without filesystem when connected through SATA?!

Is Seagate using some proprietary way of storing the data when using the drive in its provided USB 3.0 enclosure? I didn’t use any kind of encryption. I just plugged the drive with USB 3.0 and started using it straight away, since it apparently came pre-formatted with an NTFS filesystem.

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The enclosure exposes the drive to the computer as an Advanced Format 4Kn device, allowing the use of MBR for compatibility with Windows XP systems. When the drive is removed from the enclosure, the change in logical sector format results in an invalid partition table.

  • External hard drives larger than 2 TiB in capacity often expose 4K sectors directly to the operating system. The 2 TiB limit commonly associated with MBR is tied to the traditional 512-byte sector size; 4K sectors are eight times as large and therefore extend the MBR limit to 16 TiB. This allows the use of MBR on disks larger than 2 TiB in capacity, enabling use on Windows XP and other systems which do not support GPT.

  • The underlying hard drive uses 512-byte sector emulation for compatibility with legacy systems. This means that while the disk physically has 4K sectors, the immediate host device (in this case, the enclosure) sees 512-byte sectors. However, to perform the aforementioned MBR expansion and enable Windows XP compatibility, the enclosure makes the drive appear to the computer as having 4K native sectors.

  • When the drive is removed from the enclosure, the 512-byte logical sectors of the underlying 512e disk are exposed. This results in an invalid partition table that cannot be correctly interpreted. The 746.52 GiB value you gave for the last "partition" when the drive is connected directly is precisely the amount of space that lies beyond the 2 TiB limit for MBR drives with 512-byte sectors.

More details about the implications of this conversion are available in this blog post.

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  • My Thermaltake BlacX dock, at least via eSATA, doesn't show my 512e 3 TB WD Green as 4Kn.
    – bwDraco
    Commented Oct 12, 2015 at 1:50
  • Thanks for your detailed explanation! I guess off-brand enclosures don't usually do this, don't they? I got an "Intenso" enclosure which (AFAIK) doesn't do this (it included a 2TB Seagate hard drive when bought). BTW, I've added my motherboard model to the original post just in case it's useful.
    – OMA
    Commented Oct 12, 2015 at 12:13
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    By default all USB enclosures don't do this, ones that do (such as the above, bundled with a specific drive) are the exception.
    – qasdfdsaq
    Commented Oct 12, 2015 at 13:04
  • I wasn't talking about empty enclosures. Of course those don't mess with the hard drive sectors. I was talking about other external hard drives.
    – OMA
    Commented Oct 12, 2015 at 18:36
  • Anyway, what would be the steps to take to properly use the drive outside the Seagate Backup Plus enclosure? Just re-partition and re-format it while plugged to my computer as a SATA drive and then copy everything over again? Is that enough or do I need to do anything extra to avoid any performance penalties when using this AFD drive?
    – OMA
    Commented Oct 12, 2015 at 19:02
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It says the drive has 3 partitions (349,31 GB of RAW data and two unassigned partitions of 1698,68 GB and 746,52 GB). This information is plain wrong, since the drive, when used in the USB enclosure, works as a single NTFS partition (2794,52 GB). How come it’s shown as 3 partitions without filesystem when connected through SATA?!

Is Seagate using some proprietary way of storing the data when using the drive in its provided USB 3.0 enclosure?

Two thoughts based on my personal experience:

  1. In my experience, the old trick of copying data to an external SATA drive in an external USB enclosure and then using it without issue with an internal SATA connection doesn’t work with drives that are larger than 2TB in size.

    Meaning the format the enclosure uses for data transfer is “oddball” or proprietary partitioning format that won’t allow a simple swap. Or maybe something else is happening? Perhaps it’s being formatted as RAID on a low level for some reason? Maybe even LVM? Don’t know since I never checked this out in depth.

    Mind you this is not the case with all external SATA enclosures, but from my casual tests the manufacturer specific enclosures—such as ones from Toshiba and Seagate—a disk formatted in such an enclosure won’t be readable by the system if connected directly.

  2. Unclear what motherboard you might be using, but not all SATA connections will allow for drives that are larger than 2TB in size. I would check your system specs to see if that might be the case.

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