I had to wait 11 weeks last year for my provisional due to medication I was taking and my gp being slow to reply to dvla 
Worst case for me was it was only short term medication and if I had waited 3 weeks to finish it it would have been quicker.
In short I am sure you will be fine but the wheels turn VERY slowly! Have you got the reference number to call and chase? Just remind them you are still alive!
Best of luck
Edit, see you have chased it. I would suggest you keep doing so