MySQL losing track of users

[Incubus]

I have a website running PHP-Nuke and MySQL database.  For some reason 
during normal operation, MySQL will lose track of the user allowed to 
access the database as well as the root user.  Editing with 
--skip-grant-tables will sometimes correct it, but not always.  Any 
reliable way to fix this and any ideas on why it loses track?

Thanks,
James

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