Strangely I went to use online check-in just now using my MP # and PIN and it said "you have too many reservations, please use confirmation number"....not had that before.
And trying to check in my wife it shows up an old passport (despite the new one being in the profile) and even checking "will be using a different passport" does not give the option to either change or verify what it may be choosing as the "different passport".
All in all, pretty unimpressed with this today I have to say.