This message was posted on behalf of Intel Corporation
Thank you for contacting Intel Technical Support,
We received your inquiry and I understand that your HDD is no presenting its full capacity, Please accept our apologies for any inconvenience this may be causing. We will be more than happy looking for a solution.
This does not seem to be an issue with the motherboard or chipset, according to your description seems that you will need to format the hard drive, in a specific way to get it fill capacity,
My recommendation is to get in contact with the manufacture of the HDD.
I would add that you need to enable UEFI support (in BIOS) to access the full capacity of drives this large.