I had a very similar problem last year Crab.
it kept refusing to allow me to start a new application because an earlier application had not been approved. (there was not such application apparent).
Eventually i called them and even their help desk could not sort it out in three phone calls.
They told me that i should just go to the medical and my AME could enter all the details from his side - which he kindly did at considerable cost of time to himself which he did not charge extra for.
Cheeky sods at CAA still sent me a bill for their fee three weeks later!!! The temptation to ask them how they had the brass neck to charge an admin fee for something they did not administer was huge - but i elected not to poke the dragon.
Used it again for my most recent renewal - worked fine.
Appreciate this input is too lat for the date threshold - sorry! Hope you got it sorted.
OH