I had the same issue as well.

Here is what the problem was for me back in June on my flight. I used a seat selection voucher for my wife. I had to phone and the person was able to fix it in seconds. While on the phone with the customer service representative, I was then able to check in. However what they did was remove all of our seat selections. I didn't notice this. And unfortunately on our return flight our seats together at the front of the plane were gone, and we had to sit in two seats a couple of rows apart at the back of the plane.

So my tip to you, if you finally get it fixed and you problem was the same as mine, ask the agent what seats you are in and make sure your seat reservations are in tact.