What exactly do you mean by "below"? If that's a modal dialog box that's monopolizing focus then you're going to need to clear it away before you're able to interrogate the window lower in the draw stack. If you log in and that window is destroyed, are you able to interrogate the lower window?
The windows popup can be traced under the windows tab of the interrogation designer page in Pega Robotics studio. Try to highlight the suspected link and see if it is the same one you are looking for, if yes then use windows application related match rules to hook it up.