Once upon a time, Tony Nelson tonynelson@georgeanelson.com said:
-a includes -P, so copying symlinks is not his problem. His problem is that the links are broken, as reported by diff.
I'm not sure what environment the OP was using to do the copy (e.g. rescue mode, live CD, etc.), but some things install relative links, which should always work, while some install fully-specified links, which won't when the FS is mounted under a different location.
For example, if you have /usr/bin/acroread as a symlink to /opt/Adobe/Reader/9/bin/acroread, but then you boot a recue mode and mount the root FS under /mnt/sysimage, the /usr/bin/acroread link will be broken.
If instead you have something like /usr/bin/Mail linked to ../../bin/mailx, it will still work.
That may be all the OP is seeing, depending on the environment used.