I checked my problem on google and also on stackexchange but could not find any solutions.
Basically this magento function is what I am using to get Price in Cart and also in Checkout from the quote Item.
<?php echo $this->helper('checkout')->formatPrice($_item->getCalculationPrice()) ?>
This always returns me the original price. In Catalog view in Product Page and in all other places special price is shown properly but not in cart and checkout.
Also totals are calculated based on original price, special price is not taken at there too.
How can I solve this issue with Magento?