Splunk will ingest the scan reports but it only reports the plugin data not that actual compliance scans. The compliance scans can be exported in .nessus .html .csv formats but the App does not appear to recognize this. is this a limitation of the Nessus API?
We had that issue as well for the .nessus files and our Splunk consultant figured out how to make it work back in 2015. We have since moved away from the .nessus files and instead just use the API which is working well and no longer requires manual intervention. We are using this with Splulnk 6.4.2 and the Splunk Add-on for Nessus 4.0.0. We plan on upgrading to 5.0.0 soon.
We configured the Nessus Add-on with two inputs. Maybe you need to configure the nessusscan in addition to nessusplugin.
We generated the two keys through the Nessus Pro GUI. We used the same keys for both inputs.
Settings, Account, click on the user, selected API Keys and then Generate.