Can you try running memtest86+ for 12-24 hours, and see if that turns
up anything?  Sometimes flaky memory can result in very confusing
problems / symptoms --- espeially when it almost but not always works
correctly.
The other thing which I might be suspicious about is if there might be
some subtle flaw (either in the design, or your specific mainboard ---
i.e., maybe a slightly cracked trace in the PCB) that is affecting DMA
transfers from the HDD, but not from the USB stick.

If you can borrow a 2TB USB-attached HDD, and try that, and that
works, but a 2TB drive attached via SATA fails, then I would be deeply
suspicious of your mainboard.

Did this ever work before?  What changed recently?  Did you upgrade to
a newer version of the distro, kernel, etc.?  Has the system been
recently moved (dropped, etc.)?  Or is this a completely new
installation?

Sorry for asking such basic questions, but this really doesn't smell
like a software bug at this point.

                                                - Ted

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https://bugs.launchpad.net/bugs/1393151

Title:
  mkfs.ext3 causes kernel panic on new WD 6 TB drive

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