Most pinned apps don't get focus in the dock when launched
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If I open an app (for this example Calculator) from the app grid that is not pinned to the dash/dock, it is active (highlighted) on the dock and I can also minimize the app by clicking on the icon. My click action setting is "Minimize or show previews" (tested also with "Minimize", no difference).
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When I pin the app (Calculator) to the dock and open it, the app is not active (highlighted) on the dock. When I click on the app icon nothing happens (can't minimize app) and it doesn't become active either. This is the case with most pinned apps, but not all. Unpin and repin the app didn't help either.
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For example, when I open a pinned Console app, it doesn't become active on the dock either. Now bringing the Calculator window back into focus, the app icon on the dock becomes active and I can also minimize it by clicking on the app icon. Then making the Console window active will also make it active on the dock. In summary - when a pinned app is opened, its window must lose focus and regain focus for the icon to become active on the dock.
For some reason, this problem does not occur with some pinned applications: GNOME Files (sometimes occurs, mostly not), LibreOffice (Flatpak), Spotify (Flatpak), Nextcloud desktop client (installed as RPM).
The problem occurred after upgrading from GNOME 46 to 47 (Fedora 40 to 41), so I assume it's a GNOME 47 specific issue. To rule out conflicts with some another extension, I started a new desktop session for testing with Dash to Dock as the only active extension, but it doesn't change this behaviour.