Dear Mr/Mrs/Ms (name),
This letter is in response to your letter dated (date), I truly understand your frustration.
We are experiencing technical difficulties at this time. We are working around the clock to ensure that our systems are up and running as soon as possible. I am sincerely apologising for any delays in refunding your money for (issue(s)).
Instructions have been given to our Bookkeeping Department and you will receive a check as soon as our systems are back up.
I appreciate your determination in settling this matter. Once again, I sincerely apologize for any inconvenience this may have caused.