Is the pinned filter getting applied to the visualization? In the lower left corner of the visualization, click the toggle spy panel button. Look at the request for the visualization. Do you see your filter in the request?
The spy panel is my favorite part of kibana. It strips away all of the magic and lets you see whats really going on ... that kibana is just a slick GUI layer and all of the power comes from Elasticsearch's amazing REST API.
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