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I'd like to know if some of you have this bug as well.
I got it since.. I don't know.. 3 years? Right now I'm riding Fedora 28, but I had the bug in Fedora 27, 26, 25, 24, and maybe Manjaro and Arch as well... As far as I can remember, I've had this bug (even if I changed my hardware almost completely during this time span).
So, the bug: at startup, once I logged in, I open (manually) a few regular apps (like Firefox, File, or Terminal) and after a few seconds (like if it's the time for GNOME Shell to warm up), the focus is blocked on one window.
First symptom: (and the easiest way to see it) when I throw my cursor in the top-left corner, I can see the blue wavy FX thing, but the dashboard is not displayed.
Second symptom: if I click on another window in the background, It isn't brought to the front. I can Alt-Tab, and the other app comes to the front, but if I click on it, the click is dispatched to the focus-blocked window.
Of course, it doesn't happen all the time, but a good 80% of the time.
Do you have, by any chance, the same bug?
Activate the subtitles for more information:
https://www.youtube.com/watch?v=ZkeRec9eiVA
Edit: And I opened a bug in in GNOME's gitlab, if anyone arrive here one day: https://gitlab.gnome.org/GNOME/gnome-shell/issues/432
But I have the same issue without any extension.