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[Solved: Theme updated] GNOME 46 grey boxes
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I'm not a Gnome expert and are using the 'dash2dock' extension, but if I right click on rightmost 'show apps' icon, and select 'dash2dock settings, I can change opacity, bg color and such.
Not sure where else to change those settings, so apol's if this is not applicable in your case.
I don't use that extension, it was the theme that had to be updated because gnome 46 changed some stuff.
Anyway thanks for helping troubleshooting!
What theme are you using?
This
https://github.com/EliverLara/Kripton)