Howdy. I opened up two photos in CS6 and tiled them side by side and added a new layer to the first one on the left. When I select the eyedropper while the left picture is active, and then click on a color on the picture on the right, I am then able to select the paintbrush and paint with that color directly on the left picture. This is the behavior I would expect. Is this what you did? Can you try the exact same thing and see if it works for you? It appears to work properly here.