If no other user have the same problem,
It should be the problem of the user account or the recive method of the user.
For user account problem, just create a new one for that user as well,
as if the recive method is POP3, it may duplicated by connection problems.
When the new account do have the same problem, try checking the forward rules.
As the user have forwarded the mail out of the server and somewere return the mail will make it duplicated.