Cannot Read files on server

I am baffled with my server, if I try to run a perl script from on the server it runs perfeclty fine. Trouble is when I try to run through the web all files will fail (-e filename) test all of them.
how can I solve this, previous days the server was running fine without problem, Do I need to configure somewhere in system files?
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sounds to me that the server has been re-configured so that the scripts are now operating under a different user and you will need to change the permissions of the files.  Or, the server administrator has changed protection of tjhe system so that it now attempts to protect the system from a script that could cause a problem and so has closed this potential doorway.

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