Hidden Folders Showing Up

I installed Leopard (10.5) on a 1.8 G5 tower. I now see folders that should be invisible. I have updated the OS to 10.5.8 and I still see these folders. This has happened a few times now on different Machines, all 1.8 G5 PPCs. Folders include, "bin", "cores", "private", "sbin", "usr", "Volumes" and aliases to "ect", "tmp" and "var".
Any ideas on why this is happening? And can I make these folders invisible again? preferably without reinstalling the OS? I do not want users accidentally deleting them or saving files into them but I already have these machines loaded with software that I would prefer not to have to reinstall.
Thanks

Open the Script Editor in the /Applications/AppleScript/ folder and run the following:
do shell script "defaults write com.apple.finder AppleShowAllFiles 0"
Click on the Finder in the Dock with the Control and Option keys held down and choose Relaunch. Some third-party utility software will also do this.
(48451)

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[Invisible Finder 2.1|http://www.versiontracker.com/php/dlpage.php?id=9867&db=mac&pid=7198&kind=& lnk=http%3A%2F%2Fwww.ragedownload.com%2Finvisfinder.sit] lists just invisible files. JuhOS X lists all files and flags invisible ones. Some applications let you toggle invisibility, though this doesn't take effect until you restart the Finder.
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