ericmark, thanks for taking time to reply
I am materials/mechanical engineer by training, I work in medical devices these days, but im not totally unskilled at electronics, its just "not my thing" . Reading back over the posts over the last few years, some of the things pasted in 2018 made a but more sense, and also, around that time I was always working away, and we only moved to the house in 2016, I never had much time to sit at the system with some of the info printed or on phone/laptop and really think hard about it/move wires aside and try and work out how the system was actually able to work. Nor did I ever get time to shut the power off to it and probe it with the multimeter to learn some more and try to work out where each un-labelled wire was going!
One thing that I hadn't grasped was the timer track in the board, was responsible for powering the stats, and once I realised that when i spent more time looking at the diagram, and reading back, then it became more clear why the upstairs system behaved weird, and also why the downstairs pump stayed powered - there was a route from a live back to the downstairs pump even when the relay was open downstairs.
I also couldn't work out how the stat and programmer were sharing cores - but i found out last night that the programmer is making and breaking the power as expected, but they have also powered the stat off that switched live locally at the wall plate, which will work, and gives a live when require to the stat, and allows it to send 240v to the central "make hot/close relays" line in the W.C.
Once I knew that, I was more confident that side doesn't need meddling with, so last night, i shut it all down, and pulled the link between the two pumps, and used that link to join the "timer 1" rail between the two W.C. I also re-made a few connections which were sketchy where 2 or 3 wires were in one side of a choc block - not nice. Why they didn't make better use of the large Live track and free connections in each zone block, or the Neutrals along the bottom, Ill never know!
That seems to have sorted a lot of the problems, but generated a new one! The boiler initially wouldn't fire up, if it wasn't late at night and I was worried about today, id have left it longer, and it may have just been it going through siphon prime mode or similar, but I also noticed that the downstairs W.C. was using the wrong relay block, so I switched that around, so the right relay was used for pump and boiler trigger respectively, and also that the polarity was the same on both WC for the boiler relays, I couldn't see why that would be the issue but seemed best practice...
And that seems to have fixed it. I did also stick the boiler on comfort always mode, and it seems to be switching in and out when demanded by the underfloor system. I did learn last night that the big combi I have, R40 , is known for not being the easiest to control, although I couldn't find any real info to qualify that it is/is not, just a bit of hearsay on a few other threads about whether or not external controls work with them or not, it seems to work fine in this install, at least now it does.
So I have essentially followed quite a bit of the recommendations from SimonH2, although for now the power will remain made or broken using the controller to both W.C., and the "hot" link will provide 240v to the timer line, instead rather than the timer powering those on both boards. Is it clean? No, does it work better than before.... yes, 100%. Will it remain like this? probably not, as there are a few changes we need to make to the house, and it will end up involving the heating at some stage, but at least I understand the oddities it has now, and that means I can label the wires up, so next time someone looks it will be clear whats what...