If it's any help, I have a 2B Mobo with 3.1 ROMS. I have partitioned & installed 2 x 40Gb 2.5 Drives & 1 x 30Gb hard drive without issue. This was using an OS3.9 boot disk & CDROM through my Blizzard IV SCSI CDROM. :mrgreen:
Prior to this I was having problems using the 3.1 hard drive installer. HDInstTool should do a better job for you & so far as this message goes which you now just tell us about, it could be in Swaheli for all that means to me.
If you are trying to use another filesystem, I'd suggest you stick to a patched & updated 3.1 FastFileSystem from here.
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