This may be an issue with your window manager. The dialog that opens to add the filter mask/layer is modal (doesn’t allow to interact with the parent window, which is blocked), and the dialog that opens to apply a filter to the image is non-modal (doesn’t block the parent window), and it looks like your window manager is treating the main window and the modal dialog as a whole.
I’m just guessing, but you could try look for that behavior in the configuration.
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