Maybe something needs fixing by apps such as Disk Warrior or something. (yes, I'm pretty specific as you can see...)
You could also try to restore some apps by poping in the CD-ROM the OS X CD

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iMac G4 OSX 10.3.9
RAM 256MB
LW 4.10.5 Basic
ADSL anything from 3 to 8Mbps/around 1024kbps

"Raise your can of Beer on high
And seal your fate forever
Our best years have passed us by
The Golden Age Of Leather"
-Blue Öyster Cult-