I too have had problems configuring MySQL in the AMP jail with "separate" ports installation of PhpMySQLAdmin.
I would recommend that we advise the pbi Team to include phpmysqladmin in the AMP Inmate
configuration, that will better guarantee tool success.
If by circumstance you are seeking to install a Web Content management System (CMS) software like MODx or Silverstripe, then these Web site applications have internal scripts that will modify the MySQL setting/setup for you.
Otherwise, for Drupal, Concrete5 and others, you need the phpMySQLAdmin installed and working correctly as part of the AMP Inmate.