Hi igiapitzakis
Thank you for the additional information.
In this specific workflow yes selecting the recurring transaction from the list will display the transaction in a new window instead of overwriting the existing one you are viewing. As far as I know currently there is no plans of changing this behavior.
Meanwhile, instead of clicking on an existing Spend Money transaction from the Reconcile Accounts window, then click on 'Use recurring' from within the transaction, it may be worth while to try opening Lists > Recurring Transactions, have the list open side by side with the Reconcile Accounts window, create recurring transactions from the list window directly, which only opens 1 transaction window and you can control where it defaults to.
Additionally, the current AccountRight platform (v20xx.x) offers Bank Feeds which saves data entry and makes bank reconciliation more convenient, it's a feature not available in v19. I would suggest checking it out as well if you haven't already.