Then you must check the customer that is used for your weborders.
If the Application Method field on the customer card contains Apply to Oldest, payments are applied to the oldest open credit entry, unless you manually specify an entry. If the application method is Manual, you always apply entries manually.
So check if the application method is set to Manually.
If that is not the case then there might be some custom code that do the posting of the payment at the same time the order is posted?