Commands apply only on mclgui windows, not on cocoa windows.
For example, Command-W, but also Command-C, Command-V, etc, are processed by the mclgui (front-window), ignoring any Cocoa window, even if it's key and main window.
For example, Command-W, but also Command-C, Command-V, etc, are processed by the mclgui (front-window), ignoring any Cocoa window, even if it's key and main window.