I think I know what is going on here, but wanted to verify. You can see in the image that the pocket is getting deeper as it does each pass. It starts at 4mm in the center and the edges are close to 7mm deep. I am using a 1/4" single flute spiral upcut bit. I noticed some burning and think a dull bit is grabbing when it starts the next step over and the upcut bit is pulling down and loosing steps in Z. I changed to another used bit and it went away for a while and then came back. I bought a similar, but 2-flute bit locally (the only thing I could source locally) and was able to run for ~50mins with no issues. Most of the topics with skipping steps I have seen are X or Y, not Z, so I wanted to check if this is plausible or if I should be looking for another cause. This is a MPCNC primo, ~16 x 21" work area, feed rate of 800mm/min X,Y and 300mm/min Z. DOC 4mm.
It also depends on the controller and drivers you are using. I am using EstlCAM as a controller and TB6600 and I had dealt with this problem for a loooong time before I figured out that I needed to change a step pulse setting because the back and forth in Z for inlays was so rapidly that it wasn’t able to process it with the setting too low. Maybe it’s something similar? The bit pulling Z down isn’t happening imo. 
I am using a Jackpot controller and Vcarve to generate the Gcode. This cut is a 4mm pocket, ~100x60mm with 4mm depth of cut, so there is no intentional z movement at all when this is happening. I need to check my coupling and grub screws. Changing the bit did seem to fix this though.
Okay, all the rest does not sound wrong, this should still not be the reason. I cut with a dull bit for ages, what is going to happen is that your parts do not have a nice edge any more, but that’s it more or less. Or it is going to skip steps, but pulling down would be a first.
As you said: Check the grub screws, that is absolutely a possibility. Besides that I am all out of ideas after having had like, one… 
I agree with this. How firmly is the workpiece attached to the spoilboard? I’m wondering if it is lifting. An upcut bit can do that.
Thanks, I will check for issues with grub screws and the coupler. The workpiece is held down well and is also quite heavy.
This is why I thought an upcut bit could also pull the Z down, either skipping steps or causing something to slip.
Yea, I mean it’s going to apply downward pressure but if that is causing skipped Z steps, there is something else going on.
Also check that the bit isn’t pulling out of the collet. I’ve had that a bunch before and it causes the exact symptoms described.
Thanks for the ideas. I will take a look and report back what I find.
I check the grub screws and gave them a tighten, but they seemed to be pretty good. I ran another pocketing job and it worked fine. Not sure what is going on, but I am about to upgrade my primo to an LR4, so I probably won’t put too much more time into this one. Thanks again for the ideas.
This issue followed me to my LR4. Turns out it was the bit slipping in the collet as @jono035 suggested. I marked the bit and sure enough it had pulled out several mm.
Sounds like you need to clean the collet out with compressed air.
Awesome, glad that suggestion helped! It’s bitten me a few times…
Have you gotten it all sorted? I think I ended up cleaning the collet, collet holder in the router and the shaft of the tool with a cotton bud soaked in acetone and that helped.
Yes, I ended up buying a new collet Thanks!
I am going to add another solution to this one. While remaking this tray, I cut the first pocket fine but while it was cutting the second one, it started going deeper again. This time it turns out that the router had gotten pretty hot and the PLA holder must have softened and stretched out, so the router was slipping down. Now there is no gap in the holder, so I will need to reprint it.
This brings up a couple of questions for me:
- Do routers typically get warm enough for this to happen? The main difference here is that I lowered the Kobalt router speed to the lowest setting to get rid of the ear piercing screech the 2 flute bit was making. I am not sure if the slower speed reduces cooling of the router also. My cut settings were 2000mm/min feed, 4.5mm DOC at the lowest rpms the kobalt does (10,000?). The first pocket to ~20mins to cut before it moved to the second one.
- Can/should the holder be printed in PETG? I don’t have any other higher temp filament right now. It seems like PETG would be fine for the holder, but wanted to check with others.
Yes, it can- and with your router running hot enough to sag PLA, you should reprint the holders in PETG.