Well, you might have a crossover model. The last MIJ ones had the V+6 format, then they switched to CIJ but it'd seem they did that before reverting to A+6. I doubt it's a fake, and even so it's just the neck. What's the full S/N, and could you post images of the neck itself?
I wouldn't worry too much, it's probably nothing serious, like I say it could be a crossover.