I can’t believe I had not tried that, but Apple support got me and now Messages works in El Capitan
There was some strangeness though, and it is to do with my NVIDIA Geforce GTX 670 I mentioned in my previous post. After resetting the PRAM the computer came back up, but all the blue was orange again, and this time I took screenshots, but they looks correct once the problem is fixed! And to fix the issue I had to re-install the latest NVIDIA web drivers, though they were showing as already installed. Next time I will take a physical picture.