I just experienced the same issue of Windows 7 seeing a smaller disk
than Linux and moving the alternate GPT header to the middle of the
partition. At first, I suspected ext2fsd, then my eSATA port. In my
case, however, it turned out that the NVIDIA nForce SATA driver was the
culprit. I had to uninstall all versions of it and get back to the stock
Windows driver in order to get it to recognize the full 3TB Seagate
ST3000DM001 drive, even though it had no problems with a 3TB Western
Digital.

Anyway, just wanted to share that in case anyone else is having the same
issue.

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https://bugs.launchpad.net/bugs/777056

Title:
  Windows 7 moves alternate GTP header to invalid position?

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