Is it possible that you are clicking on the reference file rather than dragging the eyedropper into it?
if you do drag the eyedropper and still have the problem, reset the tool and see if that helps.
Thanks for your reply. To clarify I am actually using the paint brush tool and pressing Alt on the keyboard to change to the eyedropper tool temporarily and then selecting the colour. I don't quite understand what you mean by could I be 'clicking on the reference file rather than dragging the eyedropper into it' as that is what I am doing, but I always have done so. To clarify, using the actual eyedropper tool presents the same problem. I am also using a tablet and pen but the mouse doesn't work properly either. How do you rest the tool? Is there an option for that in the preferences? One final thing. I think this problem may have occurred since the last update and since the colour wheel feature was added that appears around the tool tip when you use the eyedropper. I have tried turning that off but it still doesn't help with the problem.
My description of the method may not have been clear enough. Perhaps this will help:
Choose the Eyedropper, click anywhere on the current image and drag the eyedropper to the color appearing anywhere on your monitor. When you release the mouse your chosen swatch will appear in Photoshop’s Foreground Color patch.
That method works with the mouse but the down side is that as you move from the current image to the colour reference image the view then scrolls completely to the side that the mouse was moved to. If using the pen then it still selects the reference file. This is very strange because I have been using Photoshop for many years and have always selected colours in this way using a pen, pressing Alt and tapping the desired colour. Before I could choose from just about anywhere within Photoshop. Even if the method you describe worked it is still more laborious than the way it used to work and slows down the work flow considerably over the course of the work.