Well, here is something strange to add to the mix. I just started printing part B of the vice base, and saw a bit of first layer patchiness. After it was finished the skin, and just starting to process the infill, I noticed that one side was starting to lift off of the buildtak mat, so I stopped it as I know it was going to go wrong big time, as the part A started curling it's toes up at me halfway through, and was slowly but surely lifting throughout the print... but held out till the end.
So I shoved my glass bed back on, removed the 0.1 z offset that I had added to try declunk the print (and added a couple layers of brim to make doubly sure ), plastered it with glue, and set it off again. Perfect first layer this time, and it isn't clunking anywhere as much as it did before when doing infill.Maybe my guess before about the magnetic bed being a bit spongy and not calibrating quite right was actually right, but isn't responsible for detaching rods! Funnily enough, I left the steel plate in this time... I used to remove it completely, and sit the glass directly on the calibration rubbers, but didn't bother this time.
Anyway, maybe this will mean something, or maybe I'm confusing... more info can't hurt right?