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I mainly have a Solaris background, so it might be different for some Linux distro's, but you'll need to use chmod with the -R (recursive) option when wanting your permissions changes to flow down into all directories and files underneath the directory you are applying the permissions to. If you have done a Chmod just on the XOops root directory, then it is most likely that the permission changes have only taken effect on the files in that directory. All the other directories will and files will still have the old permissions.
