This happened to me twice last week. I had checked in online for SFO to IAD and got switched from an aisle to a different aisle. Strange, but that didn't make much of a difference. On the way back, I got rerouted thru PHX and there even with an aisle BP in my hand, I get nabbed at the gate and stuck in the back on a window seat. I just love it when the GA plays dumb and say "Oh there must be something wrong with your check-in." Seems like to the web check in application doesn't mean anything... sometimes.