Prepare your Queries!

global $wpdb;
$wpdb->get_results( 
    $wpdb->prepare( 
        "SELECT %s blog_id, last_updated FROM %s WHERE public="1" AND archived = '0' AND mature="0" AND spam = '0' AND deleted ='0' AND UPPER(blog_name) LIKE '%s' %s %s ", ARRAY_A 
    ),
    $extra,
    $wpdb->blogs,
    $wpdb->esc_like( 'A%' ),
    $order,
    $limit
);

Never ever send data without prepare! Also: There’re some functions like like_escape() that’ll help you preparing the data properly.

Still wondering why you’d want to search for something like A%…