I've definitely had that happen before also. I think what happened is that I didn't press the button that says "Confirm Seats" right after I'd selected them. Btw, I also switched to an exit row seat, and it did ask me the questions before bringing me back to the seat map. I must've clicked on continue or back or something that didn't confirm the seat when I went back to printing the boarding pass. Luckily, I noticed it right when I printed out the BP, and called up. They were able to switch it manually, and I just reprinted my BP at the airport. It's possible that at 1AM, just waking up, you didn't notice the "Confirm Seats" button, and just continued checking in without the seats actually being confirmed in the system.