I bought Fences a while back, and back then I had a Windows 10 Home version, where this problem also persisted.
At one point, I switched to a dual-monitor setup at which point the problem seemed to subside for a while.
Just a couple days ago, the problem is back, and just today I've figured out that the problem is Fences.
Now, I can't properly reproduce this problem but I've uninstalled Fences and the problem is gone. The thing is, I can't live without Fences and so I need this problem fixed quick. The details are; when Fences is on (perhaps with some buggy setting I had off for months/etc), often times it will select one program for focus (seemingly randomly) and not let me focus any other program for use EXCEPT if I ALT+TAB and use my keyboard. Once I click it or anywhere else on the screen, focus is lost to everything. If, for example, Notepad.exe is focussed and I go to click Task Manager, both Notepad and Task Manager will be unfocussed, unselected.
The best way to visualize this, is that Fences is putting up an invisible overlay that you cannot click through and covers the entire screen except for the program it chooses.
This problem can be temporarily alleviated when ending the explorer.exe process (at least, for the most part), because Fences injects dlls into it. Next, when explorer is off and considering rundll32 is still running, the problem persists EXCEPT when I specfically ALT+TAB to Task Manager and click that window. Once this happens, normal focus is restored to the screen until a few seconds after I activate explorer.exe again through Task Manager. After explorer.exe is opened again, and after a short though seemingly random interval, focus is lost again - but it seems to usually be triggered when I open a web browser or some other application.
I found, in the case of the web browser, neither left or right click would work but the scroll up & down worked - however this is not true for Steam chat or Task Manager - scroll did not work in those two program windows.
I can't think of any more information to give - when this happens, no amount of mouse use will affect anything on screen (except the 'selected' process), no clicks, right clicks, moving anywhere, no link hover effects, nothing.
My full specs for this PC are below. I've had the program on Steam for a few months without this issue, and I'm not sure what caused it to start up again. I really hope someone can solve this problem, and quick.
Intel i7-3770 CPU @ 3.40 GHz
Windows 10 Enterprise 2016 LTSB (Build 14393)
This is my support ticket which is now 'closed' - I'm pretty sure I was directed to the forums by automated response for this issue.