I have a strange case, too. Booked ZRH-ORD-ZRH in F as an award for 2 persons, both SEN. I selected 1D/1G on both flights, but for some unknown reason the 1D seat allocation for the 2nd person on the return flight was silently ignored.
On swiss.com I can no longer edit the seats for that flight and see the message: "This option is not available for your flight. For further information please refer to our Conditions seat selection". Since we are both SEN and this is First, I do not think it is a condition issue.
I called the Swiss SEN hotline yesterday and they promised me to change that (it could take a few hours), but checking today nothing has changed.
Since I do not expect that anyone will prefer 1D (with a stranger sitting in 1G) over a window seat, I am sure it will work out at the airport.