I have splunk set up on a few redhat boxes, and I am getting duplicate events from them. One event will list the hostname as the FQDN which is fine, because thats how it is specified in server.conf.
The duplicate event is being indexed as host equal to simply the hostname.
What could be causing this?
You most likely have the same monitor defined in two configuration files. Run the following command(s) and check for duplicate inputs:
./splunk list monitor
./splunk list tcp
./splunk list udp
server.conf probably has nothing to do with this. [default]host=