Problem solved. The issue was the APRS-IS port didn't have the IS to RF port checked. The RF port did have it checked and packets were hitting the tracefilter from the APRS-IS so I didn't think there was an issue from the APRS-IS side.
My other instance didn't work but for that one it was easier to delete the conf file and start again from fresh rather than troubleshoot.
Your previous message is very useful and I've archived in my email inbox for future reference. I would be useful to have that iGate troubleshooting list on the wiki.
MB7UCM / MM1PTT