I checked the message processing setting thru the API-Browser to make sure 
all Graylog nodes have the correct settings.
They all report back

{

  "processor_order": [
    "org.graylog.plugins.pipelineprocessor.processors.PipelineInterpreter",
    "org.graylog2.messageprocessors.MessageFilterChainProcessor",
    "org.graylog.plugins.map.geoip.processor.GeoIpProcessor"
  ],
  "disabled_processors": []
}


So still the open question... what is going on with the GeoIpProcessor and 
why is it ignoring custom fields.

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