Floor Softening--what Could the Problem Be?

Perhaps you should have a termite inspection? Carpenter ants can also cause structural damage, and they can sometimes start at roof level if they can drop down out of trees. I'm not really sure what else might be a cause of a structural problem. Perhaps a condensation problem might cause moisture to collect somewhere between the floors? I'd move my son to a different room to be on the safe side. You might have to find a way to get a look at the joists in that part of the house in order to figure out what's going on.

By softening do you mean the floor gives more when you step on it than it used to? If that is the case the flooring below the pergo may be warped/warping and the give would be from the extra space between the two. I would call a contractor to see if they can give you a free estimate on the fix. They may know something else that would be causing it as well.

at my inlaws house, it was termites. i'd get an inspector to come look.

Is there a bathroom next to his room or maybe the roof leak down th wall to is floor? I don't know I would call someone to come check it out though maybe theres something not aware of