You could write and say there's no way you could have had any training on JPA during your time in, and therefore it's unreasonable for them to expect you to understand what was going on in your pay statement. In fact, as you were under pretty intensive training you were relying on your specialists to ensure it was correct and had been lead to believe it was - you had other things to worry about.
They won't pay any attention but your letter and their reply will be of great interest to your MP. You might not even have to go to your MP, just tell JPAC you're thinking of it and who knows, all your problems might go away overnight.
The Citizens Advice Bureau give good advice on things like this, and might even know a good solicitor who will pull apart JPACs argument if need be. It shouldn't get that far, so don't worry about that just yet, you can drag this out for ages until you have got the ATPL, are earning pots of money and then promise to pay them back at five pounds a month...
Good luck!