Just to add a data point to this issue. Flying back from AGP yesterday myself and my other half with a lap infant were booked into seats 3D/3G (on separate bookings, wife and infant on an avios booking). When checking in online, I got 3D no problem but bizarrely my other half when checking in despite showing 3G during the process when the boarding pass issued it showed 31E!
I rang EI and they said the booking still shows 3G as reserved for her but it was under airport control so check at the desk in the airport. At the airport check in desk we were able to get 1A/D, the agent said as it was an infant booking that 3G was not allowed so she had to move us. I'm not sure what the difference is between the seats or why we were originally able to select them with an infant on the booking but just to watch out.