This is in reference to the letter dated (date). After reading your letter of (date), I can thoroughly understand why you are running out of patience.
While it would be easy to place the blame on our computer, this poor fellow has received enough abuse since joining our firm. After all, he only follows the orders that are given to him. Therefore, I would really request you to please accept my apology for the delay in refunding your money for (basis of adjustment)
Our accounts department has been instructed to issue a check to you at once, which you should be receiving within a few days.
I am grateful that your letter was brought to my attention and I appreciate your perseverance in settling this matter. I assure you that I am personally looking in to this matter now, and will resolve all the issues. Once again, I am very sorry for the inconvenience this has caused you.