If by "blank" window, you're referring to the "Differences" window, then it means it's appearing because there are still some entries within - for example, Skip, etc but are not listed because of your display filtering. In other words, it may appear to be blank but it's actually not empty.
You can enable the option to prevent the Differences window from appearing by going to:
Modify > Expert > Compare Options > Do not show the Differences screen if it is empty...
You can enable the option to prevent the Differences window from appearing by going to:
Modify > Expert > Compare Options > Do not show the Differences screen if it is empty...