I just checked my certificate of recognition and it states that I finished my course when I passed my last module aswell, and it seems as though it's a 3 years course.
I think thats a common practice in the 147 schools to state that the course was completed at the last module passed.
Having said that, I wasn't turned down by the UKCAA when I applied for the license.
I would still advise you to check your paper work, form 19 and logbook and make sure they state that you had done a 2 years experience and a certificate of experience from the employer.
phone call the UKCAA aswell if needs must and speak your problem with them.