My advice would be to write to the highest authority possible in your service.
Three weeks after I left the RN in Jan 2002 I got a letter from MoD Accounts stating that due to "belated receipt of information" I owed Her Majesty's Royal Navy the sum of £13. This after having made several visits to my UPO prior to leaving to ensure that everything was in order, which I was assured it was. I sent them a cheque, enclosed with a very snotty letter.
But I also received the very same week the customary "thank you for your service" letter from the Second Sea Lord. So I wrote him a letter thanking him for his, and commenting on the above and what I thought of. Something along the lines of "their is no excuse for the Officer of the Watch having the ship late at an RV, despite what belated information he or she maybe in receipt of".
2SL wrote me a second letter, in which he explained how he had investigated the matter personaly and that is was a disgrace and that I should not have had to pay, and that the necessary corrective action had been taken etc etc.........