Line 53 in my minicart.php is this one:
PHP Code:
$MINICART["total_items"] = ((!empty($cart["products"]) and is_array($cart["products"]))?count($cart["products"]):0) + ((!empty($cart["giftcerts"]) and is_array($cart["giftcerts"]))?count($cart["giftcerts"]):0);
}
maybe you changed it somehow?
I've attached my minicart.php for you. It's the same version as you are working with. I've tested it and the gift certificate works, though it just adds to the totals rather than looking like a product in the minicart.