I just booked an award ticket this morning, and I saw that my seat selections (but not the preference in my profile) that I made in the booking process were completely ignored. Also, after again choosing my seats for each segment through the itinerary page, hitting 'save & exit' didn't save all of my seat selections for all of the segments - I had to 'save' each seat selection separately.
Browser: Google Chrome 7.0.517.44