Another shot into the blue, what does "getent passwd | grep 1000" say?
Do you use any kind of remote user database (NIS, LDAP, etc.), or is
this a fairly standard desktop install? If you don't have any secret
user names or home directory names, would you mind attaching your
/etc/passwd and /etc/group (NOT /etc/shadow, that has the encrypted
passwords!) so that I can see whether I can reproduce this with these
files?

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https://bugs.launchpad.net/bugs/1451815

Title:
  lists users multiple time when requiring user authentication

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