alanburke [alanburke]

  if ($result =='00') {
    $comment = t('Paid by Realex online for order #!order, Transaction #!transid , Batch #!batchid', 
   array(
    '!order' => check_plain($orderid), 
    '!transid' => check_plain($pasref), 
    '!batchid' => check_plain($batch)
   ));

Using the right placeholder, there is no need to call check_plain().

    $output .= uc_cart_complete_sale($order);
    $output .= '<h3>' . t('Payment Successful!') . '</h3>';
    $options = array();
    $options['absolute'] = TRUE;
    $output .= '<h2>' . l(t('Click to return to website','<front>', $options)) . '</h2>';

I guess it should be l(t('Click to return to website'),'<front>', $options).