I also was having this problem – sometimes the residuals won’t show up and I couldn’t figure out why.
Then I figured it out. It was because I had the wrong component selected, and the images weren’t registered in that component. A single image will have different residuals for different components, and no residuals if you’ve selected a component in which it is not registered.
The fact that which component is selected affects the behavior of everything was extremely confusing to me at first. I think this needs to be emphasized more to the user somehow. For example, the Selected input(s) panel has a Registered (True/False) property and I always figured that this told me whether or not the image had been registered into any component. It doesn’t – it tells you if the image is registered in the currently selected component, which I found totally unexpected.