A relative of mine who works in Border Force says that the chip can be corrupted over time and thus cause the rejection. But the officer on duty will NEVER tell you why the system or officer supervising the system, rejected you. If they did, you might be able to 'game' the system.
I only get through about 30% of the time and it varies by airport. On a recent trip to VCE, at VCE their computer handled my e-passport without a pause. Returning to LHR = rejected. Consequently, I have decided never to bother with the computer again and just go to the human queue.