I was Googling identical problem and managed to solve it myself so I thought to share my finding although this thread is old.
It seems that HDToolBox under 3.9 is doing something really funny when adding SFS filesystem to the RDB while partitioning a fresh drive. I installed a new drive in my BPPC and when I physically removed the internal IDE drive, the machine would crash on boot.
Lucky me, I also checked out the filesystems in the RDB with HDInstTools and for some reason, it seems that HDToolBox had set the dostype of SmartFileSystem as CFS\0 instead of SFS\0. Changing that and also removing FFS 45.9 (I don't use it at all) seemed to fix all problems and now my computer boots nicely from an external SCSI drive.
Rgds,
Mikko.