I had a similar problem with my initial class 1 whilst I was serving in the Royal Navy. When I joined I was amongst about 25% of the entrants who passed all their fitness tests at the first attempt having followed the pre joining fitness programme.
I was referred to the respiratory specialist at the CAA for further testing and examination. It was found that I was entirely fit and healthy, just that my lung capacity is outside 2 standard deviations of the norm. I was given a full unrestricted class 1 medical and recently gained my fATPL.
Get further consultation - there maybe nothing wrong with you other then what I had. I can run quite a respectable 5000m, it would be all the more respectable with slightly larger lungs!!