Thanks for all the advice! I phoned up and it seems they no longer liked the connection time between arriving in LHR and departing for JFK (it was only 70 minutes or so) - however the agent (after some gentle suggestion) kindly booked us both on to a much nicer GLA - LHR flight - no positioning to DUB required on the way out, with the rest of the itinerary staying the same. So now we've got GLA-LHR-JFK-PHX-SFO on the way out - much better!