You said that permissions are correct, but for which user?

Make sure that you can run your scripts from the command line as the exact user that your webserver runs under. In UNIX if you do not have permission to view a file then the OS will sometimes return a file not found error.

If you know the file exists and you hard code the path and the server still cannot find the file then the problem is probably one of a lack of permissions for the user under whose account the webserver executes.