Hi Floyd,
I suspected as much.
The problem is due to the way Linux addresses the scsi hdds (ie. sda, sdb, sdc etc.)
If your drives were in the correct ID sequence (ie. Boot = ID0, 2nd HDD = ID1, etc) then there would most likely be no problem (because HDD1 = sda, HDD2 = sdb, etc).
If there were only one drive, SME would automatically call it sda even if it were on ID2. But when you added another drive with a lower ID, I'm guessing that Linux then assigns sda to the HDD with the lower SCSI ID (thereby rendering your partitions all mixed up because there are not where they should be anymore), and thus not booting correctly anymore.
Kelvin