Come to think of it, I've noticed the same thing when selecting/assigning seats. On checking in, it's vital to hit "confirm.." to be locked in for the new seat (if you choose to change it).

However, recently (for flights w/in the last 6 months or so) I have noticed that I can no longer change seats via the "Manage Your Flight" link. This is upsetting, as I see the seat map, select a new seat, hit confirm, etc., get a new confirmation up with the OLD seat still listed! It used to be where you had to change the seat only over the phone for an existing booking. Then, they added the great feature which I enjoyed for about 5+ months, and it blindly disappeared - I think it's more of a glitch in the system, but a big one that has not yet been caught.