Since I have upgraded to version 5.0 I keep receiving the above message in the yellow bar at the top of the web gui. My question is twofold, is this intended and if so how can I disable this, or is this a bug.
Have you enabled clustering on your indexer? If so, that warning message will appear if you're receiving data from a forwarder that doesn't have indexer acknowledgement enabled. You can ignore the warning, although for most purposes it's recommended that you do use indexer acknowledgement with clustered indexers.