I would like to think the police officers that protect our Royal Family would all know what these people look like
Could it be that the officers involved had been drafted in from another section/detail/unit to beef up security following the two (?) previous incidents and had never actually met the DoY. Yes, they may have seen photographs but often when you meet someone for the first time you think you would recognise from the media, films or briefings etc they seem different because they are shorter/taller/fatter etc than you imagined (particularly given it was night as well [I think]). That split second of is it/isn't it could have been all that mattered - better to be safe than sorry??
How many times have you seen a "celeb" and done the is it/isn't it conversation? I bumped into Paul Merton in an HMV store and took a double take as I didn't realise how tall he was "in real life".