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WTaskbar 0.14
Fixed: a minimized window keeps its own button. With ungrouped buttons, minimizing a window of some apps — WExplorer among them — replaced its button (for example "Downloads") with a plain app button ("WExplorer"). macOS sometimes reports such a window as a dialog while its app is in the background, and the taskbar skipped it. A window that can be minimized is now always shown as a window. This replaces the 0.13 attempt, which did not fix the problem.
Install: download wtaskbar-0.14.dmg, open it and drag WTaskbar to Applications. The app is not notarized, so on first launch go to System Settings → Privacy & Security → Open Anyway, or run:
xattr -dr com.apple.quarantine /Applications/WTaskbar.appRequires macOS 13 or later.