I would claim from ATW ASAP now. Id certainly enclose an explanation for the delay in claiming and perhaps a copy of the letter from Merseyrail as proof of their back log. I wonder if ATW would be more inclined to issue RTVs for an out of date claim?
I am disappointed that ME did not provide a cheque refund or a goodwill gesture. You are entitled to have your complaint looked at again by a Manager at ME if you wish, before you complain to Transport Focus.
1) The difference was £8.
2) Responsibility for checking the correct ticket has been issued falls to the customer - it is like this in every walk of life. Check your change, make sure you've picked up your shopping, etc.
3) The OP was given a £10 voucher - more than the difference in the first place.
The customer has no recourse to a cheque refund. NRCoT:
2.4 Once you have bought your Ticket, you should check that you have the correct Ticket(s) for the journey you intend to make. If you think a mistake has been made by the Train Company or Licenced Retailer that sold you the Ticket, you should tell them as soon as possible.
While the OP did inform the company as soon as they could, really this ought to have been done at the time. The train company are under no obligation to refund any difference - indeed, they have no proof that the ticket submitted to them was actually used by the OP at all. It might have been one found on the floor, or bought for a friend not entitled to a discount.
The OP has been dealt with satisfactorily (bar the very long wait) and this should be the end of it. Suggesting the matter should be escalated is self-defeating and frankly a waste of everyone's time.