The guys at passport control all tell me there is no issue with the chip in my passport either but over the last 2 years I have tried the e-gates at Manchester, Heathrow, Gatwick, Glasgow and Edinburgh and none of them, ever, have worked for me.
I fly into EDI about once per month, but no matter what you say to the jobsworths before the passport desks they insist you queue for the e-gates despite the far more helpful guys from immigration saying to go straight to them in future. I'm guessing that is because Edinburgh have monetised the passport queues with a paid for fast track and the EDI employees don't want to let someone into the country without them getting their extra few ££.