I'm having pretty aggravating problems with my WD15EARS and WD20EARS sata hard disks running with my Gigabyte 880GA-UD3H motherboard (http://www.gigabyte.us/products/prod....aspx?pid=3758). I'm booting off of a smaller seagate sata drive and I manage to start up in about 45 seconds from grub to login (also odd since I'm running a 6-core 3.2ghz processor). When I connect either of the WD Caviar Green drives the boot time shoots up to about 3 and a half minutes, which is clearly unacceptable. Additionally, all methods of installing any version of ubuntu onto the drive fails because it appears that it would take more than a day to finish. I've lost my most dmesg log, but I'll try to grab a new one and post it soon.

Once the drives get booted properly I can manage to read and write to single files with approximately expected speeds, but booting, mounting, and running LS on a drive lag beyond all expectations. I've checked the drive with WD align and attempted to format it several times with partitions starting on the 2048, 64, and 63 sectors with no performance increase using NTFS or EXT3/4. My Windows Dual-boot boots up a bit slower with the drives, but nothing close to 3.5 minutes.

Is this drive incompatible with recent Ubuntu distributions (I'm trying 11.10 and 12.04)? Does the motherboard have known issues with SATA III? Has anyone had any luck getting help from WD on this type of issue (I bought the drives on EBay, so there's probably no warranty)? Any information you can provide would be much appreciated.

The closest thing I've found on the forums to this issue is linked below, but although the hardware is similar they seem to be experiencing different symptoms. They're also using Caviar Green and a gigabyte board, but can't seem to even have the drive appear in the BIOS.
http://ubuntuforums.org/showthread.php?t=1968693