I just had a similar experience two days ago. I flew in from DEL, and had about 1 1/2 hours to kill before my connecting flight to LHR. So, I go to the lounge, and then to the Airbrau outlet in T1 (never left airside). So now, I've got to go to G47, as the LHR flight is boarding.

A security checkpoint??? Now I'm stuck in a line, and the German woman in front of me (it must have been her first flight) has got like four carry ons holding everything that was in her household, so she takes like 5 minutes (she is S L O W). Next, I go through. I forget about the bottle of water that was in my carry on that cleared at least four airports in India (JAI, BOM, GOI, DEL). Anyway, I had to get rid of that and then on to the LHR flight. I was the last pax to clear the gate (I got a small chiding by the gate agent for being so close on time, as the aircraft was parked at a remote stand). Oh well, I made the flight and got off on time. But, I have no idea what that secondary security check was for. It was for all passengers, even those who would have started in MUC.