For not having VAT on shipping cost if the conditions about VAT intracom are OK:
in catalog/includes/modules/order_total/ot_shipping.php, find these two lines (about 52):
$shipping_tax = tep_get_tax_rate($GLOBALS[$module]->tax_class, $order->delivery['country']['id'], $order->delivery['zone_id']);
$shipping_tax_description = tep_get_tax_description($GLOBALS[$module]->tax_class, $order->delivery['country']['id'], $order->delivery['zone_id']);
and replace them by:
// BOF for TVA_intracom_v3.4
if ($order->billing['company'] != '' && $order->billing['tva_intracom'] != '' && $order->billing['country']['id'] != STORE_COUNTRY && $order->delivery['country']['id'] != STORE_COUNTRY) {
$shipping_tax = 0;
$shipping_tax_description = NO_TAX;
} else {
// EOF for TVA_intracom_v3.4
$shipping_tax = tep_get_tax_rate($GLOBALS[$module]->tax_class, $order->delivery['country']['id'], $order->delivery['zone_id']);
$shipping_tax_description = tep_get_tax_description($GLOBALS[$module]->tax_class, $order->delivery['country']['id'], $order->delivery['zone_id']);
// BOF for TVA_intracom_v3.4
}
// EOF for TVA_intracom_v3.4
Just be carefull and check if it's OK but I think it is: it's just put the VAT on shipping as '0'.