I've seen the exact same problem with desktop grade drives. The only sure fix, is to use enterprise-class drives. The list of drives that should work 100% of the time is at http://serverconfigurator.intel.com/sct_app.aspx#/SctTHOL/16723/Intel%C2%AE%20Server%20Board%20S3420GPLX%20(S3420GPLX)
Well the problem happens with both enterprise Seagate Constellation SATA 1TB/2TB too.
Would a single desktop drive be affect the function of the whole sas module?
I will try and do some testing for our next server and see if that is the case....