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I have also run root kits to try and find any issues
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Explain this? ^
Anyhow, Things to try: Edit sudoers file. Disable/enable root user and set your preferences (lock remote desktop) from there. Now a bit more invasive; boot single user, use .SetupDone to make admin user if needed. All logs can be viewed via the console. If the remote-sharing box is unchecked chances are your ok. Install outbound/inbound firwalls or sentry. ipnetsentry is boss. Yea. That should do it.
-Digitol-