Shutdown on X = startup error on 9



was wondering if anyone could help me out w/ this. i use unix all the time but this was puzzling me.
system is a dual g4/450 256mb, 9.0.4 and X (1H39) installed on same partition..

i have no problem switching startup disks in 9, then rebooting to bring up OS X... but when i shutdown X to go back to 9, 9 usually tells me i didn't shut down properly and runs the disk checking utility. this is starting to get annoying..

this is how i shutdown X: from a term, as root (of course)
i just sync; sync; shutdown -h now

any clues?
I was getting the same kind of errors if I did not shutdown the classic environment before shutting down OS X.