Which version of the MonoGame PCL did you build against? I ask because I believe the EmptyKeys 3.0 release on NuGet is bugged. Older versions of the MonoGame PCL - the one they have on public NuGet included - had a strange bug where on certain screens - I think high DPI - the mouse location is incorrect. At the top of the screen the mouse clicks are accurate, but as you move down they become more and more inaccurate and you are unable to hit screen elements unless you move your mouse way below their actual screen location. This affected Windows Desktop MonoGame only. I saw this in my own personal project and was instructed by MonoGame developers to use the private NuGet server located at: http://teamcity.monogame.net/guestA...vice.svc/.
That fixes the issue.
I downloaded the UI_Examples for EmptyKeys and the Desktop Windows sample does indeed have this issue. It is only seen on certain machines, but does occur on my HP Spectre x360 laptop. I am investigating using EmptyKeys for my application, but I cannot do so until it is rebuilt with this issue fixed. The MonoGame PCL on nuget.org is way out of date compared to the current version on their private feed.