Well, from their point of view they never received payment.. you might never have sent the cheque, just wrote the stub and ripped up the cheque. Do you not reconcile your bank statements.
I'm not sure if you should have received the penalty points but that may be the correct procedure. Are you entitled to reminders?, it may be that they don't send them..
I'd say you will be treated nicely.. you may have to go to court on the day, and the Guard may say on your behalf that there appears to have been an error, that the fine has now been paid, and that the Guards consider the matter closed and would be happy to have the case closed..