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I have the same problem. I edited the template in International > Translations > Emails > order_conf and changed the {total_shipping} for {total_shipping_tax_excl}. And also, I updated the PaymentModule.php and I added these lines 

'{total_shipping_tax_excl}' => Tools::displayPrice($order->total_shipping_tax_excl, $this->context->currency, false),
'{total_shipping_tax_incl}' => Tools::displayPrice($order->total_shipping_tax_incl, $this->context->currency, false),

in 

     // Send an e-mail to customer (one order = one email)
                    if ($id_order_state != Configuration::get('PS_OS_ERROR') && $id_order_state != Configuration::get('PS_OS_CANCELED') && $this->context->customer->id) {
                        $invoice = new Address((int)$order->id_address_invoice);
                        $delivery = new Address((int)$order->id_address_delivery);
                        $delivery_state = $delivery->id_state ? new State((int)$delivery->id_state) : false;
                        $invoice_state = $invoice->id_state ? new State((int)$invoice->id_state) : false;

                        $data = array(
                        '{firstname}' => $this->context->customer->firstname,
                        '{lastname}' => $this->context->customer->lastname,
                        '{email}' => $this->context->customer->email,
                        '{delivery_block_txt}' => $this->_getFormatedAddress($delivery, "\n"),
                        '{invoice_block_txt}' => $this->_getFormatedAddress($invoice, "\n")

.

.

.

                        '{total_paid}' => Tools::displayPrice($order->total_paid, $this->context->currency, false),
                        '{total_products}' => Tools::displayPrice(Product::getTaxCalculationMethod() == PS_TAX_EXC ? $order->total_products : $order->total_products_wt, $this->context->currency, false),
                        '{total_discounts}' => Tools::displayPrice($order->total_discounts, $this->context->currency, false),
                        '{total_shipping}' => Tools::displayPrice($order->total_shipping, $this->context->currency, false),                                                                                                                                '{total_shipping_tax_excl}' => Tools::displayPrice($order->total_shipping_tax_excl, $this->context->currency, false),                                                                                                  '{total_shipping_tax_incl}' => Tools::displayPrice($order->total_shipping_tax_incl, $this->context->currency, false),
                        '{total_wrapping}' => Tools::displayPrice($order->total_wrapping, $this->context->currency, false),
                        '{total_tax_paid}' => Tools::displayPrice(($order->total_products_wt - $order->total_products) + ($order->total_shipping_tax_incl - $order->total_shipping_tax_excl), $this->context->currency, false));

Can you help me? Where is the problem? Thank you so much!