For multiple monitors, if there is different scaling, the PowerPoint 2016 Pen (ink) won't draw in the correct place if using an attached Wacom tablet. Solution is to set the scaling to be the same for every display.

From this page

I found the solution to the single screen problem for Surface PRO 3 running Office 2013 Powerpoint on Windows 10

You need to go to Settings/System/Display

Then slide the "Change the size of text, apps, and other items: 150%"

change the slider to 100%, and then enter presentation mode, and the pen works!

It does seem to be a Powerpoint issue where in presentation mode it is confused by the DPI scaling setting. It probably also replies to the original reporter's issue where the screen scaling DPI settings are not universally 100%