For what it's worth, I finally managed to resolve this problem, though I'm still not sure what happened or whose fault it is...
When I installed OS X server, I had two extra disks in the machine (Seagate 9 Gb cheetahs) that were, for the time being, unused. I had hoped to make those into a single RAID array after upgrading to 10.1, with its support for RAID in the Disk Utility. One of these had previously been formatted in HFS+, the other for Linux.
It seems that something in the 10.1 upgrade process destroyed the linux-formatted cheetah. When I took these drives out of the machine, and put them into another 10.1 (client) machine, that machine also developed the "can't start up in OS 9" syndrome. When I removed the (formerly) linux-formatted one, that problem went away. As far as I cvan tell, the cheetah is now a paperweight, and worse...
Even after removing the extra drives, my OS X Server 10.1 machine couldn't be booted into its OS 9.2.1 partition, though. What I did to fix this was (a) install StartupDisk 9.2.3 [from the OS X 10.1 _Client_ upgrade disk) in the System Folder of the 9.2.1 partition; (b) startup from my OS 9.1 install CD; (c) use the StartupDisk control panel to set the 9.2.1 partition as the startup disk; (d) reboot, at which point the machine started up correctly from the 9.2.1 partition, (e) use the StartupDisk control panel (9.2.3) to set the 9.2.1 partition as the startup. At this point the machine would correctly restart from either the 9.2.1 partition or the OS X server partition, depending on which was set by (either version of) StartupDisk.
So I conclude that my problem was a combination of (a) damage done to the non-Mac-formatted cheetah during the OS X server 10.1 upgrade process; and (b) OF changes, which were eventually undone once I had started up from an OS 9 CD. Alternative interpretations are welcome....
The problem that the 10.1 upgrade apparently makes OF changes which have as a consequence the impossibility of booting into OS 9 has been reported for various machines in various forums, as I have discovered since posting this. I have seen no mention of this on the major Mac sites, though. I hope someone with more understanding of just what's going on than I can bring this to Apple's attention.
--Steve Anderson