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I got some answers and it's complicated. "QoE is using “something like” wireshark (exactly pcap driver and 3rd party library that tries to classify traffic by rules to application/protocol name). In some cases (usually when there is only oneside communication) library is not able to classify it correctly because of missing handshake or active transaction so it assigns it to some application only by port used." Therefore, if the service is showing data but no transactions, there is a higher rate of false positives. If SolarWinds is seeing transactions and data, then "false positive classification is very uncommon."
8888port is for the freenet proxy software where you access most freenet functionality from the browser. Port
8080is for the Freenet Message System if you install that and
9481is for the API interface that jSite uses." according to Using Freenet .
Thank you SolarWinds support and devs for helping me with this.