Im experiencing the same "problems" since i have a very similar
configuration to yours.

2 * 1.5TB in raid0 by the MB ich10r fake raid controller used as media
storage.

But im afraid to let parted fix/move the gpt backup. I dont know what
the result would be for windows.

Since i did some other stuff i shouldn't have and already lost the 3TB array 
and spent like 2 weeks to try to get the data back and then I ended up 
rebuilding the partition with TestDisk in windows.
Under linux with kpartx TestDisk failed to find the partition.

Technically (as i understand) if the backup GPT  partition table is not
at the end of the disk its not that bad since it is still mapped as used
sectors and wont be overwritten. I might be wrong tough.

I also read somewhere that macs hfs had some problem with this as the
disks last sector is not writable and GPT standard/guideline states that
the backup table must be there.

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

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

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