Since you have SCSI the first thing I'd like to ask is - have you been
using HDToolBox and Phase5's SCSI_Utils?
Two RDB prepping tools being used on the same disk is extremely
dangerous and can give you system messages such as "Error - Disk Block
-128,659 is out of range" as they have different standards for
specifying size ranges in thr RDB.
If you have used two prepping tools then I think it'd be best to save
stuff and re-format the drive.
OS3.9 should have the <4Gb thing fixed... and also the <1Gb per
partition that the old HDToolBox stumbled on.