New machine bogging down / missing steps

[EddyCurrent]

I think you are running the spindle too slow, 16500 to 18000 sounds better, also the depth of cut seems high, and your feedrate is too high.
So I would try this to see how it cuts; speed 18000rpm, depth of cut (with 4mm dia.tool) 2mm, feedrate 800mm/min.
If that works okay you can try to increase the depth of cut and feedrate until it starts to fail.

. . .but i guess the extra mass combined with hitting a hard bit of plywood could be enough. It occured to me thT the x axis is cutting accross the grain, and the y is cutting down the grain, which might explain why the y axis seems ok.

Plywood has grain going at 90 degrees to each other in adjacent layers so there is no 'with' or 'across' the grain.