Turning Hardware Acceleration OFF seems to be the setting that affects popups & dialogs.
Chrome was continually hiding Dialog Windows when I needed to respond Yes or No to things, also when I needed to Rename folders in my bookmarks panel. After weeks of doing this. I disabled all the Chrome helpers in Settings, Also In windows 10 I switched Window Snapping off. It has done something to put the popups and dialogs back in the Viewport.
When this bug is happening, I was able to shut a tab by first pressing Enter before clicking the tab close X button. The browser had an alert box, hidden which needed a response from the user.
Switching Hardware Accleration Off and back On, Killing the Chrome process and switching all the other Helpers Off and back has fixed it for me... It must be in chrome itself because Ive just gone into a Chrome window in the Mac and it has now stopped the problem, without any intervention. Im guessing flicking the chrome settings on/off/on has caused it to reposition the dialogs. I cant get the browser to repeat the fault now...