I'm giving you my opinion, which is more or less the same as everyone else who has replied to you.
I've been caught out many times by forgetting to pay on time, my own fault, I paid the penalty and got on with it. It seems that you have issues with pre-paying for trips and the system not matching these payments to the trips you took afterwards. They have said that they will be looking into this for you and this sounds pretty reasonable. From experience of using the M50 everyday and having the odd issue with the toll that was beyond my control, the company who look after the payments has always resolved any issues for me.