I have a similar situation. I booked my flight with a travel agent and when I attempted to claim back the taxes I was told that no refund was due at all. I then challenged them to explain where the taxes go and the travel agent responded by saying that the carrier (Virgin in my case) withhold the tax when a ticket is cancelled. I spoke to Virgin Customer Services and Virgin said this is absolute rubbish - all taxes are refundable to the travel agent to pass on back to the customer. In my case its obvious that the travel agent have no intention of returning my money back. I have written off to ATOL to get some advise but it seems the rules around refunds of taxes are quite vague such that they allow travel agents and airlines to pull a fast one if they can get away with it.