The non-determinism in which identifiers are shown might be a bug in the installer, or it might be caused by failure of ID commands to the drives.
I think most of the problems you're still having must be caused by a bug in the RAID driver, mpt2sas (or its firmware, if that's not embedded in the BIOS). Thanks. Please let me know how I can report the potential bug(s) and what I can do to help track them down. Jeff (http://engineering.purdue.edu/~qobi)