A few more details.... Actually, I still don't have all the information, but I have a much better picture.
Here's my setup:
OS: Windows Server 2008 R2
HDD: Western Digital 2002FYPS
Raid Controller: 3ware 9650SE 24ML
Array: RAID 6 (14 HDDs)
Here are the error logs from my RAID controller.https://dl.dropbox.com/u/10737837/lsi.Win2k8R2.HOMESERVER.072412.10704.ziphttps://dl.dropbox.com/u/10737837/errorlog_0.dat
A few nights ago, the array reported that there was a problem with two of the drives (drives 0 and 5). I'm not sure what the exact error was. I was in the middle of a relatively large transfer (~50GB). All of a sudden, my system froze for about 2 hours, and after that, I managed to do a normal restart. The controller does this sometimes - kicks out two drives randomly and then proceeds to rebuild them.
When the system started, I checked 3DM2 (the raid controller software). It said that the array was degraded and proceeded to automatically rebuild the array. Everything was fine until the rebuild process hit 14%. Then I received several errors concerning drive 3 (which is strange, because the two drives that were dropped are 0 and 5). While the rebuilding process is still listed as "active" under 3DM2, it hasn't progressed at all overnight.
I took drive 3 out of the array and ran the WD diagnostics software on it:
I also tried reading the SMART data via HD Tune: