I believe your problem is your motherboard. I ran into the same problem as well on an X58 chipset board with ICH10R (ASUS P6Tv2). In your BIOS under the Storage Configuration, I was able to set it to RAID and upon exiting I went into the RAID utility and setup 5 1TB HDD in a RAID5. I wanted to use a WD Velocirator as my system drive. The only way I could get Server 2008 R2 to install was to change the SATA to AHCI. Server 2008 wouldn't install on anything else. I found out later that the only way the RAID 5 was going to work was in the OS as a software RAID5 using Intel's Storage Matrix Manager. I was also limited to 2TB. I lost the remaining 1.6TB of space. Unfortuantely, while the i7 processor rocks, RAID5 is limited to 2TB and not the 256TB Microsoft would have you believe. Your only choice to use a true RAID 5 is to get a Hardware RAID5 Controller card in use either the PCI or PCI-e slots.
Server 2008 requires AHCI just like Windows 7. x32 or x64 it does not matter. RAID 0,1,5,10 requires RAID to be set in the Storage Configuration. You can't have both and it's annoying. I could be off, but that's what I have been able to conclude. Someone please correct me if there is a viable alternative.