Hi Kevwefreeborn,
With two open trades for the same pair suggest to me there are two instances of MetaTrader trading the same Expert Advisors. The reason why only one trade is closed in this case is because the Expert Advisor looked for the magic number of the open trade and closed it. The Expert Advisor thinks it did it job because it only opens one trade at a time and therefore does not look to close a second position with the same magic number.
Alan,