I almost don't want to mention this, using driver1 (a supposed good one) I did an extended test for the graunchy sound, after about 5mins of up and down (still just the long axis, no gantry) it started to make a bit of a noise.

This leads me to think the ballnut is fine and the noise is related to the drive problem. Driver2 starts to breakdown(?) quickly, Driver1 breaks down after longer time. I don't know what I mean by break down, maybe a heat thing? (I'll put my hand on the heatsink next time).