As MJ says, MOR the Instructor. Did you verify the Instructor was actually a JAA Instructor? As Instructors and Examiners we shoulder the responsibility to learn the rules and apply them correctly.
I have seen it a number of times where the Instructor has signed the licence. Invariably it has been Instructors in the US who have done this as they are used to working on a different system.
Your class rating is indeed invalid and all the flight that you have done since the rating lapsed have been technically illegal. The LPC will resolve the problem.