In options (Alt-O) on the Filters tab make sure Guild Chat is set to Show. In the windows, filters can only be set to one window, you will see a * next to filters set for specific windows. So it wouldnt be possible for any filter to be enabled in multiple windows
If you did want to reset everything, you can hit /load, select your UI, click on 'Keep Your Layout' to uncheck/not highlighted and then load Skin
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