I have had the same problem, but I paid over the phone. When I recieved my notice to pay €94 I rang to say that I had paid for the journey. I e-mailed them a copy of my bank statement to show the payment had left my laser card account. I got another letter saying that they had investigated and couldn't find the payment. I then wrote to them enclosing a copy of my bank statement and my phone bill showing the exact date and time I made payment. Same result. I have posted off another letter, but this time I am requesting any and all informatioin held digitally by them in relation to me, under the Data Protection Act. So far, no reply, but I can still see the disputed payments on the web site under my reg number.
They are the worst company I have had the dispeasure to deal with and I re-route through Lucan most of the time now. Dig in your heels and don't give in. It's up to them to prove you didn't pay, which will be hard to do if you have a receipt. They should look at the shop in which you paid for any compensation.