@avamander Thank you for your suggestions.
Your advice is good and I have already done a lot of what you suggested. I didn't put a scope on it, I may make another portable system and try that then as I do not see any pullups on the pro mini nor on the pi3 schematics. That could well be the centre of my problems.
I also stumbled upon this page ...... https://spellfoundry.com/2016/05/29/configuring-gpio-serial-port-raspbian-jessie-including-pi-3/
This also seems to pinpoint issues with serial on the Raspberry Pi 3B, and why they happen. Seems the foundation made changes that have had a detrimental effect on serial comms stability. It would explain why this happened after 'upgrading' from Pi 2B to Pi 3B. It seems conclusive to me that the issue is with the RPi 3B serial port not working correctly.....Live and learn I guess
Still, for the last 4 days I have been running with a serial to usb adapter and no ghost nodes and no data spikes on the graphs. I wonder if there are pullups on the board? It's difficult to see clearly with the plastic wrapper on it!
Things are looking very hopeful right now though...
The only issue I still face is random loss of data from some nodes. The outages can be just one value report missing (Most nodes send data once every 5 minutes), right up to over 6 hours of data loss. Then suddenly it all starts working again. I might have more time now to look into that a bit morenow the system is stable again, but it is so random.
I did also find quite a few 'less than good' dupont cables (from China) - So I have soldered directly a lot of connections now or modified/re-crimped the cables that were 'iffy'.
Thanks again to you and Jkandasa for the support and help. I am nearly there with this now and can build some more nodes with confidence.