It does seem a little harsh that CBT prior to Class one issue causes big problems but I know that CBT after issue is much less serious. How come?
They (well, one CAA doctor) tried to prevent my initial Class 1 due to childhood asthma even though I had servred as a pilot in the Navy!
Sadly there sometimes seems little rhyme or reason to such decisions, it is up to the whim of the particular quack who had control of your file and like mine if he is ex RAF and has an irremovable bug up his arse about asthma and flying than flying you will find hard to achieve.
Keep at them politely but firmly to find out if there really is a medical impasse or just a paper jam. If the former think about getting an aviation specialist second opinion. (PM me if you need a contact)
Good luck.
btw, three months isn't really a long time for the CAA medical people...