Gift Card payment ignores points payment and is charged whole amount

When I make a payment using both gift card and by redeeming points, both the payments go through but my gift card is charged the grand total instead of (grand total-rewards currency amount). On the cart calculations are done properly but this problem only arises after I press confirm order. Is there a specific way I should be handling gift card payments because right now I am just adding it to quote programmatically like so:

private function _setGiftCard(&$quote)
{

    try {
        $cards = unserialize($quote->getGiftCards());
        foreach ($cards as $card) {
            $currentCard = Mage::getModel('enterprise_giftcardaccount/giftcardaccount')->load($card['i']);
            if ($currentCard->getId()) {
                $currentCard->removeFromCart(true, $quote);
            }
        }

        $giftCard = Mage::getModel('enterprise_giftcardaccount/giftcardaccount')->loadByCode($this->_giftCard);
    $cid = $this->_getRead()->fetchOne('SELECT customer_id FROM do_customer_giftcard WHERE giftcard_id='.$giftCard->getId());
    if($cid!=$this->_customerId) throw new Exception('no ownership');
        $giftCard->addToCart(true, $quote);
    } catch (Exception $e) {
        throw new Goopter_Gift_Card_Exception($e->getMessage());
    }
}

Order Details after confirming order: Order Total before payment was $48.58, used $45 from points and gift card should’ve been charged $4.58