Does your problem start after trying to boot to your internal 9?
I've had similar issues lately (not on my machines, luckily). On one system I was able to fix it by running the OS 9.2.2 updater via Classic. For whatever reason, once the boot command had been issued to to the (apparently) bad OS 9 install, it mucked everything else up. Booting into X allowed alternate boot methods with the exception of the bad(?) 9 install.