The problem could have been caused by the particular model of HDD you have. Unfortunately Intel doesn't have a "List of Drives that Don't work" just a list of drives that do work and your particular model isn't listed (check http://www.intel.com/support/motherboards/server/ss4200-e/sb/CS-028561.htm).
i doubt you'll get your data back on this situation. the system seems to be creating a brand new configuration instead of rebuilding the current RAID.
the "The file system preparation" is what the system does when you insert brand new drives on the unit. it formats them, creates new partitions and builds a filesystem. after that it synchronizes the RAID.
Best thing to do to avoid any future problems:
1. use tested drives.
2. connect them to the system and wait for the unit to build the raid.
3. update the software on the unit to 1.1.11.x http://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&Inst=Yes&ProductID=2910&DwnldID=16295&strOSs=38&OSFullName=OS%20Independent&lang=eng
4. once the update is complete, remove the drives, clear the MBR on them and reinsert them. This will cause the unit to build a new raid configuration but with the new firmware already installed.