One thing does come to mind. Could you not have got him to check you in for the 1st leg ( which he had already started ) and then check in for the next flight separately when u got there rather than going off to get flights changed?

What they did seems odd since they semeed happy to do the AY flight. Perhaps they are sticklers for the rules when it comes to the US flights. They don't want to risk any comebacks if something is wrong.

If it comes to trying to get money out of them, I wouldn't bet on it. They do hold all the cards in this. They can show what time you tried to check in and show that this was outside the minimum check in time and so were allowed to refuse you.

Dave