I don't know if this problem is widespread, as I haven't noticed any topics related to it, but I've seen it now on a pair of computers, both iMacs (one Rev. A, the other Rev. C).
After installing 9.0.4, at some point you'll notice that the computer says your entire hard drive is empty: i.e., for a rev. A iMac, it claims there are 4.1 GB available, even though the files are clearly there and will run if you click on them. If you restart, the dreaded question mark folder appears.
I rebooted from the System 9 CD and ran Disk First Aid. It found one minor problem with the Volume Header and fixed it at once without hassles. I restarted, and the computer found the System Folder immediately. I've had no trouble with this odd Volume Header confusion since I first fixed it on my Rev. A; just today I fixed it on my mother's Rev. C.
Hope this might help if the problem crops up elsewhere.
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