Similar issues happened on me last Oct on a flight from GRU/IAD/SFO. When I tried to get on IAD/SFO flight with my pre-issued boarding pass, the agent said my boarding pass was not valid. I was reported as no-show on GRU/IAD flight and my tickets were cancelled. I did not have to argue that much that I was on the GIG/IAD flight, but my upgraded first class seat had been already assigned to someone else. Luckily there was a last minute no-show for first class and I was able to get that seat for the long flight.