One thing I've noticed is that if you configure the agents on Linux and then later you re-run the configuration again it doesn't seem to update things properly.

Is this working as designed?

Like you'll end up with double entries in your gwha.conf file and the rcscripts won't be right

I'm referring specifically for the MTA/POA

So is it better to just delete the files and let it recreate or edit them and fix the bad/old stuff?