The motherboard will determine whether it enumerates locally connected HDs before RAID-connected HDs. The only thing I can suggest is attach all your HDs first, before installation; or only add new HDs on the RS2BL040. Also make sure they're on the list at http://www.intel.com/support/motherboards/server/sb/CS-031815.htm , to avoid future problems.
For the firmware problem, I could only recommend flashing the firmware again. Did you run it from Windows, or DOS, last time?