I've been searching as best I can for this precise problem, but the only place I found it exactly was here, and I don't think that the OP ever got an adequate answer. Most of the issues I've seen with regards to 3TB hard drives stem from outdated hardware, dual-booting issues, etc.
My server is brand-new, using an ASRock H67M-ITX with onboard Intel RAID. I have two Seagate 3TB set up in a RAID 1 array. Everything I can see in the raid controller indicates that the motherboard is having no problems with this arrangement: both disks show up as 3TB devices, and the RAID array does as well. The only point at which anything goes amiss is upon loading 12.04-desktop-amd64 from a flash drive, and attempting to partition. At this stage, I create a new partition table on the disk, and the resulting size is 801567 MB.
I was under the impression that the motherboard had no problems with RAID arrays this large, and also that the latest long-term stable release of 64-bit Ubuntu shipped with in-kernel GPT support and would have no difficulties as well. Any ideas on what I'm doing wrong?