I have done some investigation on this issue and the problem is the following:

When the quote items are loaded as a collection, it assigns the products to the quote items, but for some reason magento is using the application store when loading the products into the quote items collection, instead of the quote store, loading the incorrect Product option prices and product option value prices (for multi select options)

This is the trace:

1. When working with the quote items, we use Mage_Sales_Model_Quote::getItemsCollection()
2. When we iterate the item collection, magento will load the items in the collection and will call Mage_Sales_Model_Resource_Quote_Item_Collection::_afterLoad() as with any other collection object
3. This method calls $this->_assignProducts() to load and assign the product to each quote item
4. This method loads a collection of products using the product IDs from the quote items and loads as well the product options for each product, specifically, in line 169, it prepares the product collection and calls Mage_Catalog_Model_Resource_Product_Collection::addOptionsToResult()
5. The problem is in this method, addOptionsToResult has hardcoded the current magento application store instead of using the store provided by the quote to the Mage_Catalog_Model_Resource_Product_Collection::setStoreId() method

The actual code for this function is:

    public function addOptionsToResult()
    {
        $productIds = [];
        foreach ($this as $product) {
            $productIds[] = $product->getId();
        }
        if (!empty($productIds)) {
            $options = Mage::getModel('catalog/product_option')
                ->getCollection()
                ->addTitleToResult(Mage::app()->getStore()->getId())
                ->addPriceToResult(Mage::app()->getStore()->getId())
                ->addProductToFilter($productIds)
                ->addValuesToResult();

            foreach ($options as $option) {
                if ($this->getItemById($option->getProductId())) {
                    $this->getItemById($option->getProductId())->addOption($option);
                }
            }
        }

        return $this;
    }

The function should be using the store in the collection instance instead of the application store. In the frontend this is not an issue since the quote store is always the same as the application store, but this is not the case in admin, where the application store is the admin store (store ID = 0), and is different from the quote store. In this case the product options are loaded using the admin store and the incorrect price, title, etc.

I will provide a fix for this.