There is an Apple TIL about problems installing 9.1 over OS X on the same partition, you may be facing something similar here. Search Apple's TIL for this article (i can't rememebr the number right now).
In the meantime, create a new folder on your 9.1 partition and move your system folder into it, then install a 'clean' system folder.
Last week, my assistant used my G4 to backup his iBook, and his system folder showed up in my Classic preference panel (it was on another partition). Also, when I had the PB, I had 9.0.4 installed on a seperate partition, and a backup of another machine in a backup folder on that partition. I was able to use both for Classic, and for booting.
It's worth a try....
PS: It is 9.1 you have, and not 9.0.4? (had to ask)
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The Man From D.A.D
[This message has been edited by batguano2000 (edited 04-01-2001).]