Intermittent problems with mouse clicks

This problem is really killing me now. It's the weirdest thing I have experienced ever on a PC. The problem occurs sporadic and never at the same time, so I am not able to reproduce the problem. Suddenly I can not click with the mouse inside certain windows. Neither left click or right click works. The funny thing is that I am still able to move the mouse around and I can still click on other windows on the screen.

For example I was running Deluge and I was organizing some stuff. Suddenly I could not click on anything inside that window. I could still click on other windows as usual, just not in Deluge

Another example is when I was running a Cubase update (an executable) I was able to click on the options and buttons until the last classic "finish" window. Suddenly I could not click on anything inside that window.

The same happened when I was using Cubase. It does not seem to matter which software or program I am running. The problem occurs completely random (or so it seems).

The keyboard is working normally even if the mouse is not.

When the problem occurs, if I press CTRL-Alt-Del and then click on the arrow button to go back in windows everything is working again. Why? I have no idea, but it seems like essential information.

I have a feeling that this has something to do with some programs I installed recently (Autohotkey, Ghost Mouse, Mouse controller and some other). I have uninstalled them all now and the problem is still occurring at times.

Things I have tried:

I have cleaned the registry with bitdefender.
Reinstalled NVIDIA drivers
Restarted computer multiple times

Please help me out guys. This is driving me nuts