I have the same issue, can be seen here: http://imgur.com/a/IFfLN
Notice how the main character (ranger, should be in back) and Aloth have moved to the front. Also Saganis wolf is now in the back.
Active formation when entering: http://imgur.com/UdDJFVa
Changing active formation makes no difference. Seems like it's only the order of the portraits that determines the formation the party enters the building in?