Windows on secondary monitor are not scaled properly.

My primary monitor is the one that gets disconnected as it is connected through display port. This tool is amazing but the problem I'm having is that the second monitor has a 125% zoom on it (as it's the same resolution but smaller physical size), but whenever the tool activates, the scale of all of the Windows are based off of the primary monitor instead of the secondary, making me have to drag each window back to the primary and then back to the secondary so that they "up-date". If this could get fixed, that would make it perfect!