I had this same issue and same solution.

I believe it was caused by using etckeeper to restore files in /etc
(including /etc/passwd and /etc/shadow).

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https://bugs.launchpad.net/bugs/45368

Title:
  Unable to unlock screen (Dapper)

Status in “gnome-screensaver” package in Ubuntu:
  Invalid

Bug description:
  Binary package hint: gnome-screensaver

  gnome-screensaver refuses to accept the user password, though the
  regular login process works fine. Need to restart X to get around the
  problem. Changing the password does not help. In constrast, when
  logged in as the root user, it is not possible to lock the screen -
  the password dialog is bypassed altogether allowing anyone to use the
  account.

  Found the following in /var/log/auth.log (when logged in as a regular
  user):

  May 16 21:42:35 localhost unix_chkpwd[15122]: check pass; user unknown
  May 16 21:42:35 localhost gnome-screensaver-dialog: (pam_unix) authentication 
failure; logname= uid=1000 euid=1000 tty=:0.0 ruser= rhost=  user=gille
  May 16 21:42:36 localhost gnome-screensaver-dialog: (pam_unix) authentication 
failure; logname= uid=1000 euid=1000 tty=:0.0 ruser= rhost=  user=root

  In other words, unix_chkpwd does not recognize my user name for some
  odd reason (in spite of both user name and user id being correct in
  the above lines), or so it appears.

  Xscreensaver has the same problem. Not sure if it is relevant, but the
  /etc/pam.d/gnome-screensaver file includes common-auth which in turn
  contains the following:

  auth    required        pam_unix.so nullok_secure

  I am able to reproduce the bug every time.

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