You did check the gears on the stepper motors were all tight.

I have to admit the auto levelling, made absolutely no sense to me and as I have a perfectly flat bed. Just levelled with my adjuster bolts for the heated bed.
But given that the first few layers are going down fairly clean.
I don't think that's the issue, still leaning towards some kind of mechanical issue.

Although if the auto levelling tells the printer the bed isn't level and to adjust for a non-level bed then that would probably be carried through the whole print.

Can anyone actually explain how the whole g29 measurements are used. I tried to follow the he3d video, but it didn't do what his did on the video and the maths made absolutely no sense whatsoever.