I had this happen to me returning from JFK as I was transferred from a late flight to an early (at no cost to myself) or face 9 hours in the concorde room lounge there. As lovely as it is 9 hours in the concorde may have been the end of me.

I spoke to BA who got me the point added within five minutes. They said its because the system takes you as a no show on the original flight you had booked on and doesn't acknowledge you on the earlier one. So you must report it manually.