The modules for column_left and column_right should be controlling these sideboxes ...

There are ways around this however depending on your template ...

Check and see which sidebox it is then do a search for the name of the sidebox file and see who all is calling it ...

column_left.php and column_right.php are calling via the select statement to the database table for layout_boxes

Also, browse the table layout_boxes and ensure you do not have a duplicate for your template ...