That's a bummer, though I'd still try not to get yourself too worried about it.
Apparently the CAA like to play things on the safe side (quite rightly) and have a tendency to go to quite extravagent lengths to cover themselves when it comes to medicals. They will investigate very minor issues very thoroughly just to make sure that what looks most probably like a non-issue really is a non-issue.
I would still take heart from the fact that NATS weren't at all bothered by it. NATS medical standards are higher than the basic requirements for the class 3 medical, so if they didn't have a problem with the reading that would suggest that it isn't likely to be a real obstacle. As I say, its probably just the CAA being careful.
I know its a crummy situation to be in. I'm in exactly the same boat at the mo - just had my initial medical for NATS, which was fine, but there's some stuff in my medical history that the CAA want to investigate more thoroughly. The doctors at NATS were quite forward and open about the fact that I could have an issue before sending me on to the CAA (although NATS weren't bothered by anything themselves), so the fact that NATS didn't think you'd have a problem is a very good sign.