Gigabyte motherboards with an Xpress Recovery BIOS are apparently affected by a bug! The following is taken from here.
“When the drive is first in the boot order, Gigabyte’s BIOS will write a backup copy of itself to a small Host Protected Area (HPA) at the end of the user area. It then hides this image by reducing the capacity of the drive by a corresponding amount. Unfortunately a bug in the BIOS incorrectly adjusts the drive’s capacity after creating the HPA. 1TB drives are reduced to 31/32/33MB, 1.5TB become 500GB, 2TB become 1TB, and 3TB become 2TB (not 2TiB).”
So a big thank you to these folks and HDAT2.