I'm going to be linking this D.O issue.
I found that when changing an attribute other radio buttons would not update properly. Specifically that when there was two possible options for these buttons but each were only available if another option in the form was set, changing the first attribute resulted in the second one not being rendered as checked. If you went to add that item to the cart the proper variation would be added so this seems to be just visual.
I was able to use xdebug to find that the default value of the buttons is set correctly.
I've been digging through the rendering trace of this element but am getting quite lost.
Does anyone know why after an ajax call a radio button would be rendered incorrectly and not be marked as checked?