OS 3.9 & Second HD

[melott]

I have an A3k with an external SCSI box which
has a CD Rom and 9 gig drive in it.
A few months ago I upgraded from OS 3.1 to OS 3.9.
When I was running OS 3.1 I could turn on the
external box when I wanted to use the CD Rom or
get something from the HD.  No Problem, the
computer would boot with or without the external
box turned on.  Now, with OS 3.9 for some reason
the computer WILL NOT boot unless I have the
external box turned on. It seems to act like a
RAID system (or my understanding of RAID).
I've looked for any settings that make this so but
can't find anything.
Can someone tell me what is going on here and
how to make the external box optional again as
with OS 3.1??

[melott]

I have 3 partitions on the external drive.
Dos-Bak, Work-Bak, and Storage.
Dos-Bak and Work-Bak are copies of the internal
drive. Dos-Bak is set to Non-Bootable, only the
internal drive (Dos partition) is bootable.
I ran this way on OS 3.1 for several years and
never had a problem, now with OS 3.9 it has to have
the external drive box running or it won't boot.
I've even wiped the internal drive (formatted)
and reinstalled OS 3.9 without the external drive
plugged in, ( a clean new installation) and it works
fine. Then when I plug in the external drive and
boot once, after that the external has to be on.
And it accesses the external drive during misc.
operations when I think it shouldn't be. I don't
think it should be accessing that drive unless
I spicifically access a file on that drive. Its like
its doing a 'RAID' system and to my knowledge
I have made NO setting to cause this. The CD Rom
drive in not causing this.
Has anyone else run into this problem??
If so, how did you solve it??