$db_prefix breaks up a certain drush configuration and certain commands

All versions up to current 6.x-3.0-rc3 and current HEAD. Multi Site problem.
On one of my boxes with drush installation, certain imporant drush commands don't work (cron, cc all and some more) to all sites that have $db_prefix. other commands ( dbupdate for example ) work fine. Site with no $db_prefix works fine with all commands.
This has been going on on this certain box for quite awhile. I've tried differnce cli configs, differnt php compiles and all of those produce similar results. Here trying to do a status command:

[root@web1 <drupalinstalldir>/sites/www.mysite.com]# drush status
Initialized Drupal 6.16 root directory at <drupalinstalldir>                                                            [notice]
Initialized Drupal site www.mysite.com at sites/www.mysite.com                                        [notice]
array_fill(): Number of elements must be positive in <drupalinstalldir>/includes/database.inc on line 253.           [warning]
implode(): Invalid arguments passed in <drupalinstalldir>/includes/database.inc on line 253.                         [warning]
array_keys(): The first argument should be an array in <drupalinstalldir>/modules/user/user.module on line 502.      [warning]
You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the   [error]
right syntax to use near &#039;)&#039; at line 1
query: SELECT p.perm FROM drupal_role r INNER JOIN drupal_permission p ON p.rid = r.rid WHERE r.rid IN () in
<drupalinstalldir>/modules/user/user.module on line 502.
 Drupal Root            :  <drupalinstalldir>
 Drupal Version         :  6.16
 Site Path              :  sites/www.mysite.com
 Site URI               :  http://www.mysite.com
 File Directory Path    :  files/<mysitefiles>
 Database Driver        :  mysql
 Database Hostname      :  drupalhost
 Database Username      :  drupal6_thissite
 Database Name          :  drupal6_thissite
 Database               :  Connected
 Drupal Bootstrap       :  Successful
 Drupal User            :  me
 Default theme          :  thissite
 Administration theme   :  slate
 PHP configuration      :  /usr/local/etc/php.ini
 Drush Version          :  6.x-3.0-rc3
 Drush configuration    :  /usr/local/etc/drushrc.php
An error occurred at function : drush_core_status                                                              [error]
Command dispatch complete                                                                                         [notice]