Applications do not focus as expected or at all but only the mouse input focus is wrong

Question

I have recently been trying to get a working Linux install on my main PC. My PC runs on a GTX 1060.

I've been having this issue where my mouse won't click properly in what looks to be a properly focused window. Instead it clicks in the window behind it or some other nonsense.

This issue occurs on the latest Ubuntu, the latest Arch, the latest Debian and the latest Manjaro. I have not tested any other distributions. The weirdest thing is, the problem does not occur on the install USB stick that I created for Ubuntu.

This is not a hardware problem as far as I can see, I have tested multiple mice and also my laptop. All have the same or very similar problems.

I think only a video will do justice to how bad this actually is but I am going to try and explain it:

Right now, I am typing in a Firefox window, it's the only application open. I cannot click anything outside the window content, I can't even drag the title-bar. The Activities button (top left) doesn't work either. Also, if I hover over the Files shortcut in the favorites bar, it does not get highlighted. The only way I can get out of the window is to ALT F4.

I cannot for the life of me figure this out. Any help is greatly appreciated.

UPDATE 1

The problem only occurs when there is multiple windows open and is slightly intermittent. The problem is there the majority of the time. It feels like the mouse is just really slow at changing the focused window.

Also another part of the problem: I can sometimes click on another window and the other window will come to the front. However the mouse still thinks it's in the old window or worse, not in any window. The keyboard acts in the (what looks to be) focused window.

Also, this problem sounds exactly the same as this super user question. Unplugging and replugging my mouse does not help though.

Answer 1

I've constantly been experiencing this as well for the last year (18.04LTS). At first, I thought it's related to Wayland, but it also happens on Xorg. GTK3 Apps are fine, but Qt, Tk, and Wx (not sure about Gtk2) ones will have the issue. The apps also have issues that the modal dialogs (popup windows inside the app) are not clickable.

My workaround is to release the mouse input focus on the app currently holding it by opening and closing a context menu (right-click context menu or the top menu).

I'm not sure if it could be related to the multi-screen setup (one 4k high dpi at 125%, one full HD at 100% and the high dpi laptop screen turned off), or high dpi in general since it also happens when only the laptop screen is used.