Adding hostnameOption=fullyqualifiedname does not resolve this issue for me either. When i view Settings | Forwarder Management I see a list of hosts reporting into the forwarder - the 'instance name' column is the FQDN but the 'host name' field is the short name (unqualified)
As i read http://docs.splunk.com/Documentation/Splunk/latest/Admin/Serverconf - i should be able to add hostnameOption to server.conf - but i don't see any difference when doing that.
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