Yes, I have had a similar problem, but with 10.1. Even after i upgraded to 10.1.2, it still would not boot from any CD or change the startup disk. The only way I was able to fix this was to physically disconnect the hard drive OS X was installed on, and force the computer to look for another OS on one of the other hard drives. After booting up from OS 9.2, I changed the startup disk to the one with OS 9.2 and reconnected the hard drive with OS X. The next time i restarted it booted up in os 9. Then i changed the startup disk, and everything worked fine, both booting from a CD and switching OSes.
To me, this sounds kinda stupid and odd, but strangely enough, it worked. perhaps some of these steps were not necessary, I just thought i'd do them anyways just in case.