Hello

I also had this problem. Here is how I fixed it.

# Call the custom function to register the checkin on each issue.

foreach ( $t_issues as $t_issue_id ) {
    if ( !in_array( $t_issue_id, $t_fixed_issues ) ) {
        helper_call_custom_function( 'checkin', array( $t_issue_id, $t_comment, $t_history_old_value, $t_history_new_value, false ) );
        email_bugnote_add($t_issue_id);
    }
}

foreach ( $t_fixed_issues as $t_issue_id ) {
    helper_call_custom_function( 'checkin', array( $t_issue_id, $t_comment, $t_history_old_value, $t_history_new_value, true ) );
    email_close($t_issue_id);
}

Basically I just added
email_bugnote_add($t_issue_id);
and
email_close($t_issue_id);

That will get your emails sending.