From what I understand, it's a (Windows) driver issue with the Intel Southbridge. As it seems, in IDE legacy mode, the entire available space of the 3TB drive is show in partitioning programs (after making the drive a GPT drive). In AHCI mode, only 700+ something GB's are shown. Intel has not come up with a driver update for AHCI modus, I don't know why. AMD's SB850 southbridge which is used on their most recent motherboards does not have this issue. And neither has the Marvell 88SE9025 SATA600-controller, which is also often used on motherboards as away to offer more than the standard 6 SATA channels. It's this Marvell controller that is bundled with the 3TB WD drive (the 3Gb/s version), on a Highpoint RocketRAID 62x controller card.

So it seems it's a (windows) driver issue, which of course is why Linux does not experience this problem. And because this Intel ICH controller is probably the one that is used on 80% (or more) of the motherboards out there, Western Digital has opted to include an alternative controller card with this drive.