It seems that your filesystem permissions are broken. Did you run a chown -R somewhere? I would probably reinstall/restore at that point?
I saw in your other topic that you used scp to transfer the files, by default that doesn't preserve modes. Did you use -p?
-p Preserves modification times, access times, and modes from the original file.
I prefer to transfer via rsync. This creates an identical structure at the other end as long as the user has the rights to create the files. (So in this case use root)