FYI, if you have any difficulty reproducing this issue, I actually
installed the mysql-server package using Puppet (version 3.8.5), not
manually with apt-get.  The puppet manifest file contains simply:

package { 'mysql-server':
   ensure => 'installed',
}
To run it, simply place the above lines into a file (say) "build.pp" and run 
this puppet command:

$ sudo puppet apply build.pp

I suspect this may be relevant.

** Description changed:

  Install the 16.04 package mysql-server and immediately run
  mysql_secure_installation to set the root database password. When
  complete, the root database password you chose doesn't work. You are
  locked out from mysql.
  
- Steps reproduce on a fresh Xenial system:
+ Steps to reproduce this issue on a fresh Xenial system:
  
  1. sudo apt-get install mysql-server
  2. sudo mysql_secure_installation
  3. Respond to the questions:
  
  - Validate password plugin?  No
  - New password: foobarblat
  - Re-enter new password: foobarblat
  - Remove anonymous users?  Y
  - Disallow root login remotely? Y
  - Remove test database and access to it? Y
  - Reload privilege tables now? Y
  
  4. mysql -p -u root
  Enter password: foobarblat
  ERROR 1698 (28000): Access denied for user 'root'@'localhost'
  
  Other people have encountered the same problem:
  
http://askubuntu.com/questions/766334/cant-login-as-mysql-user-root-from-normal-user-account-in-ubuntu-16-04

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https://bugs.launchpad.net/bugs/1610574

Title:
  mysql_secure_installation locks out root database user

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