This option enables you to specify if a "Editor is not focused" alert message should appear if the user calls tinyMCE.execCommand and havn't selected a editor instance before. This message will normaly not appear unless some integration has been made. Using tinyMCE.execInstanceCommand prevents this from happening since it auto focuses the editor specified. The default value of this option is "true".
Example of usage of the focus_alert option:
tinyMCE.init({ ... focus_alert : false });