Have recently encountered an issue with prices in Magento Checkout appearing doubled. There are a number of solutions online which seem to (in various combinations) do the trick.

A particular cause of the error seems to be when more than two addresses appear in the sales_flat_quote_address table.

Disable Third Party Checkouts

This seems to be the best solution, the issue predominantly happening when a third party one page checkout extension is in use.

Dave Boyce Solution

This code removes anything other than two addresses being pulled for a quote from the table sales_flat_quote_address. The quick fix goes in Mage\Checkout\Model\Cart.php.

In The Mage_Checkout_Model_Cart class init() function enter the code below the line: $this->getQuote()->setCheckoutMethod('');

$addresses = $this->getQuote()->getAllAddresses();
    
if (count($addresses) > 2) {
  for($i = 2; $i < count($addresses); $i++) {
    $address = $addresses[$i];
    $address->isDeleted(true);
  }
}

Multiple Address Checkout

It should also be check that under System > Configuration > Shipping Settings that “Maximum Qty Allowed for Shipping to Multiple Addresses” is set the value to “0”. The default is 100.

To fix, change “Allow shipping to multiple address” to “Yes” and Save. Then Set Allow Shipping to “No” and set Maximum Addresses to “0”. Click Save.

Magento

Magento is a feature-rich ecommerce platform built on open-source technology that provides online merchants with unprecedented flexibility and control over the look, content and functionality of their ecommerce store.

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