I'm still at a loss to explain this. I've had no plausible explanation on the Canon forum. Suggestions were atmospheric effects, convection currents, smoke (this is a building in progress so I don't know if there is a heating system on yet which might have some kind of hot air rising...). The effect doesn't look like this somehow, but I may be wrong. It looks like shifting moire, not anything moving up vertically in the air.
Tried some very similar shots today and the moving blotches were not there. I used Live View very quickly to focus and no more. I shot with window open and closed - made a little difference to detail resolution but not much otherwise. No UV filter. So just air between the lens and the subject.
What I do notice is that the battery drains rapidly in Live View. So I'm wondering if it is:
1) Low battery effects
2) Sensor is overheating in Live View
My suspicion is that it's something to do with the electronics and the behaviour of the sensor when Live View is left on.