in email/inc/class.boindex.inc.php 

changing   
                        $this->xi['auto_refresh_widget'] =
                        //      $my_other_widgets->auto_refresh(
                        //            
$GLOBALS['phpgw_info']['flags']['email_refresh_uri'],
                        //              240000);
                        $this->xi['auto_refresh_widget'] =

to this                              
$my_other_widgets->auto_refresh(
                                      
$GLOBALS['phpgw_info']['flags']['email_refresh_uri'] );

makes the system use the user pref.

Adding $GLOBALS['phpgw']->msg->set_pref_value('refresh_ms',
10*60*1000 ); at the top of the auto_refresh function in
email/inc/class.html_widgets.inc.php works, but I can't
figure out the prefs screen to get a text box to show up for
this setting.