Paul, It happens more frequently than you'd think with races. I remember reports of a 10km race a few years ago that was 400 m short as well, and everyone was breaking their PB, and many of the more experienced athletes realised there was a problem at the time. Anyhow, luckily they had sorted out Manchester this time, so it didn't affect you this year. It's kind of unforgivable at a major marathon though. It just shouldn't happen. How the calibration mistake wasn't picked up by a double check at the time I do not know.
At least the London Marathon organisers have been nice and still allowed GFA entries next year for 2015 GMM times, just by adding 2 or 3 mins onto finish times. Still crazy that this happened, and went unnoticed for 3 years!