I've tried to shutdown both ways with the same result.
As I remember the problem started when I shutdown through WEBGUI for the first time.
Today I updated firmware but it not helped. I tried to reset to factory settings, no result. All disks formatted ext3. Tried to connect NAS to router and directly to my computer, same problem anywhere. Next week I'll buy 3 more WD's hope it will help.
Also I metntioned that WD is cool but both Hitachi are relatively hot.