After 10.4.5 we are getting ? in the Dock and disappearing software

We use a bank of Macs all Mac X 10.4.5 yesterday one Mac displayed question marks in the Dock and the resulting software iLife had disappeared out of the Application folders. Today on a totally separate Mac two question Marks appeared in the Dock and we see that applications Peak Dv and drop Stuff have disappeared again the software is not in the applications folder.
The network is a closed loop and not accessible by third party other than the Internet.
any advice??????????????
Dual 1 GHz PowerPC G4 Mac OS X (10.4.5) Qusetion marks appearing

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After 10.4.5 we are getting ? in the Dock and disappearing software

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