Hmmm...

The install SQL, all the way back to the original version, contains the auto-increment, and some indexes, but yours doesn't.
Without the auto-increment, all the insertions of records for each setting, including when the "reset" button is used, are getting a value of 0, which is why the links are giving strange results on screen.

This is how it should be, from the v155 install SQL:
Code:
CREATE TABLE layout_boxes ( 
  layout_id int(11) NOT NULL auto_increment,
  layout_template varchar(64) NOT NULL default '',
  layout_box_name varchar(64) NOT NULL default '',
  layout_box_status tinyint(1) NOT NULL default '0',
  layout_box_location tinyint(1) NOT NULL default '0',
  layout_box_sort_order int(11) NOT NULL default '0',
  layout_box_sort_order_single int(11) NOT NULL default '0',
  layout_box_status_single tinyint(4) NOT NULL default '0',
  PRIMARY KEY  (layout_id),
  KEY idx_name_template_zen (layout_template,layout_box_name),
  KEY idx_layout_box_status_zen (layout_box_status),
  KEY idx_layout_box_sort_order_zen (layout_box_sort_order)
) ENGINE=MyISAM;