Just had this. Flight booked last month, 3 UK passengers (same family) with UK passports, all in BAEC with passport details on system, on a BA holiday flying on BA metal from LHR to GIB.
2 passengers could get a boarding card, one could not. No issues at the airport (other than it was an unnecessary queue as we all had carry on). Just checked in for the return - same problem. Passport obviously checked only a few days ago now. The IT is poor (half the time it can't even show upcoming bookings in your BAEC account).