I am using the following code to set the product to the quote object
$product=Mage::getModel('catalog/product')->load($id);
$quote->addProduct($product,new Varien_Object(array('qty' => $productid)));
The product and it's quantity is stored in the sales_flat_quote_item
table on saving the quote but the price and base price is 0. The price is not set with the price of the product.