You called the river, so, what did he have?
I would have reraised the flop to find out if he made a set on you. Often, when people in the blinds want to represent that the flop helped them, they call the pre-flop raise and bet the flop. He check-raised you which makes me think he outdrew you somehow. They bluff check-raise usually when they think you're doing a continuation bet. I would have reraised his reraise on the flop to see where you are in the hand.