Why do the amounts on some orders show a different currency code?

Every order is saved in the currency the customer checked out in. The order page and list show that currency's code after each amount, such as "49.00 USD".

That happens when your store offers more than one currency (the Multiple Currencies plugin) and the shopper switched currency before buying. The amounts on that order stay in their currency for good, even if you change your store's currency or exchange rates later.

So the figure is what the customer actually paid. Invoices for that order use the same currency.