I have noticed this in the past too, but I kept at it.
I just changed my seat yesterday- no problem.
Are you clicking on "modify" under the seat selection?
I did notice that there was a difference in terms of the seats between the page that says "manage your booking " and the actual page where you make seat changes...and I think it was because they switched planes from the time of ticketing. I hit the modify button, and it showed a different seat map, which I took to indicate that the plane had switched. I switched my seats, although "mange my booking" showed the old seat, my boarding pass showed the new, and confirmed seat that I took once I boarded.
They still show the old seat number on my flight intinerary.
