Ready to throw logstash config file out the window -- help please :)

Thank you so much for the reply.

I was starting to think that may be the case.

So i just move the if's outside like so:
if [type] == "syslog-relay" {
output {
elasticsearch {
hosts => "localhost:9200"
index => "logstash-%{+YYYY.MM.dd}"
}
} else if [type] == "netflow" {
output {
elasticsearch {
hosts => "localhost:9200"
index => "flowstash-%{+YYYY.MM.dd}"
}
}

?