Usual preface, I’m with PreciseBits so while I try to only post general information take everything I say with the understanding that I have a bias.
I kind of doubt this assuming that this is posted in the right section and I understand the hardware used. Normally when people worry about this it is due to loosing steps. With the Masso and closed loop you shouldn’t be having that issue. Mechanically the other things that come to mind are something is loose and able to move (spindle mount, tool in the collet, etc.) or deflection. From the pictures there’s sections that look like steps where the height change stays at the new level. That wouldn’t be deflection as the load across the piece wouldn’t account for that.
I’ve also seen where software or the controller does this when the plunge speed doesn’t match the feed. Some of our customers that do production work like this not only set the plunge and feed the same for the finishing pass but also have set their accelerations to match. Not sure how much this would help in this case as both of those depend on hardware, CAM, and controller. For the same reason I won’t go more with this right now.
I’m going to preface this next one as I seriously doubt it being the issue. Wood can warp from cutting it. There’s a bunch of listed reasons for it, moisture content, surface stress, nature of wood grain, etc. You might want to check if your piece is warped or cupped though. The reason I doubt this is the issue is you glued the whole board down. There could be some movement in it still as flexible and inconsistent as wood is. I would be surprised if the results looked like this though. Solutions to this vary from skim cutting the surfaces to pocketing the back. I’m dubious of how effective these are.
Two things I would do regardless.
First change your finishing from raster to anything else. Offset or maze are usually much more consistent (and less obvious when they mess up). If you have to use raster try to offset it by 45°. Both of those should result in a better finish even without the issue you are having.
Second, like Chris said… feed faster… a LOT faster. Any time you are running less than 50% of the tool diameter you run into chip thinning. This is basically where you are cutting a smaller chipload (feed) than you would be at 50% or greater. It gets worse the smaller your stepover gets.
To give an example lets say we’re cutting at 100IPM with a 2 flute tool at 10KRPM. Your chipload for that would be 0.005" (Feed / RPM / flutes). What that means is that the thickest part of the chip that each flute is cutting per rotation is 0.005" thick. Now let’s say that you are only taking a 20% stepover. To get that same chip size you need to cut 1.25x the original or 125IPM. At 8% this becomes 1.84x, 184IPM. At 4% it’s 2.55x, 255IPM.
The reason this is important is that cutting too small of a chip will lead to more heat and a poorer finish as there is a minimum size chip needed to actually CUT and not just rub or grind the material out of the way. Assuming the machine has no issue with the feed, the forces for compensating for chip thinning are about the same as the 50% stepover (some changes from chip form). This is because the forces (and your resulting deflection) are determined by the cubic material removed per rev per flute (chipload and pass depth).
Hope that’s useful. I’ll post back if I remember any other things that have caused this type of issue. Otherwise, let me know if there’s something I can expand on or help with.