In some cases when Phoenix CashOnDelivery [http://www.magentocommerce.com/magento-connect/cashondelivery.html (extension in magento connect)] is used together with OneStepCheckout the applied COD amount dissapears when ajax update is called or order is placed.

This issue relates to totals element collecting in CashOnDelivery payment method and the fact that the implementation of this is meant for magento 1.3 series and not updated to follow slightly newer 1.4 API. To patch this please use the contents for PhoenixCashOnDeliveryModelQuoteTotal file from https://gist.github.com/speedupmate/2300993