Just came home from work, couldn't wait to test it.
It's fixed! I repeat: the focus issue is not present in beta v.16.11!

Just clicked through 6 opened windows a few dozen times, while bringing Nexus to foreground in between. Not a single stolen focus happened.

Great work, Jorge! I've learned only machine programming (cnc), so my understanding of the compexity of this whole thing is limited, but I can imagine that it wasn't an easy task. Considering all the variables, and... uhm, MS Windows.

I hope you can "focus" on other things now. Hehe. (sorry) ^^

Can you imagine that another bug is also related to Nexus? Sometimes a random window sets itself to "always on top".
Does somebody else who use Nexus have this issue?
And since the Windows OS by default doesn't have a function to enable/disable this, the only way to disable it, is installing a third party tool that can change it.

I have this issue right now in Vivaldi browser. And since Vivaldi has some kind of custom frame, the third party tool I have installed to change that status doesn't work in Vivaldi. (it's usually accessible from the window frame, but in Vivaldi it's not shown)

So I'm back to looking for the root of this issue...

Was this already present or is it a new issue?

EDIT: Let me explain how 'pop up on mouseover' works so you can understand better what *might* be causing such an issue:

So, the idea behind 'pop up on mouseover' is to temporarily bring a dock above all other windows even when it is partially obscured/overlapped by the foreground window.

You hover the pointer over the little bit of the dock that can be seen and, after a user-specified (normally very short) delay the dock becomes fully visible by raising itself above the foreground window.

Now, the big advantage: if you don't click on the dock (you just wanted to see something or you didn't actually want to raise the dock) all you have to do is move the mouse pointer away from it. The dock is then sent behind the foreground window, and everything is as it was before. No need to click on anything or look for empty spaces to click on.

Now, when the dock comes forward on mouseover, it does NOT do this by becoming the active window (i.e.; the window with the keyboard focus marked as active in the taskbar). Instead it comes forward by tricking Windows into changing its position in the z-order: the dock is briefly set to 'always on top' (which brings it above all other windows) and immediately set again to 'normal z-order'.

When the user moves away from the dock without clicking on it, the same trick is applied, but this time to the window that was previously above the dock (i.e.; the foreground window) and is now partially obscured by it. It is quickly switched between 'always on top' (which brings it back above the dock and all other windows) and normal z-order (so it does not remain always on top).

The bug affecting you that was fixed in the beta of v16.11 happened because Nexus was doing the above to the *wrong* window, i.e.; it was raising the window that was the *previous* foreground window instead of the window that had just become the *current* foreground window (in reality the bug was a bit more complicated than that, as the dock was triggering the change of the z-order of another window before even having to, i.e.; almost as soon as the mouse pointer cruised above it!)

From what I understood, the issue you are reporting now ONLY affects the Vivaldi browser (never heard of that browser until you mentioned it, by the way). And that browser also seems to have issues with a general tool used to set/reset the z-order of windows because, according to you, it uses some kind of custom frame.

It can be argued that the problem is not Nexus this time, but Vivaldi not correctly responding to SetWindowPos messages.

Thanks for the explanation.

Yes, this is a diffenert bug. But it's not limited to that browser. I've mentioned the browser, because I can't apply my regular fix on it. So it gave me one more reason to find the cause of this bug.

It happens at random to random windows. It could be windows explorer, web browser or just a properties window.
This issue is present since about the time the focus issue appeared. That's why I thought it might be related.
What it makes so hard to identify the cause, is the extreme randomness, reaching from every few seconds to every few days...

1. More or less how often is 'random' in your case?

2. Does it go away if you disable 'Pop up on mouseover' ?

3. Also, probably not related at all, but do you use WIN+D (Show Desktop) a lot?

Using the beta versiyon for two days, I think problem is solved. But now I have another off topic problem. When I use "show folder in menu" option for a folder some of my shortcuts are not working (when I click, nothing happens) and their icons are default windows shortcut icon. Do you have any idea?

1. It's really like I've said. It can be every few seconds, so that the bug literally "jumps" from one window to another, or on the same window over and over, and somtimes I don't have it for days. Maybe it gets triggered by a specific action, but I couldn't find out what.

2. You mean "show dock on mouse over" - the same function that caused the focus bug?
I'll try - but it means that I can't use my dock properly for maybe days.
But first I'll wait if 16.11 has maybe fixed it already. The last time I've had that bug was right after installing 16.11. It could have been the "last trace" of the bug.
As soon as the bug appears again, I'll disable "show dock on mouse over" and observe it a few days, to find out if it has anything to do with Nexus.

3. No - I never use Show Desktop.

It's 3 days now without the "always on top" bug. That's a good sign.
It was rare that I didn't seen it for that long.

I think it really was a side effect of the focus bug. Like I've mentioned, the last time I've seen it, was right after updating to 16.11. And the affected window was opened the whole time, from 16.9 to 16.11. So it could have had the bug from 16.09 still in it. And after closing it, the last traces of the bug were gone.

Good! Lets cross our fingers and hope you're right.