I'm confused what was wrong with your seat on your new BP? Why not change it with the agent there if you weren't happy?

What happens (I've experienced it personally) is that once you are checked in, my itins does not reflect seat assignment changes. Any attempt to change the seat screws things up royally.

Now, you should have been able to go to easy check in online and mess with things. It should have showed checked-in. If it was asking for certs, I would not have touched a thing.

You should be able to cancel your check-in online too, regardless of where you orginally checked in at. If you can, do this and try checking in.

But this whole checked in thing that the agents are giving you is crap. I've never had problems upgrading, changing, cancelling or anything else on an itin I am checked in on.