When I run a program, often, when the running router touches the board, there is a noticeable “clunk”, then the z axis is off. This most often happens at the start of the run, but can happen during the middle of the project. I can reset the z axis, and the program will then run, with or without an ensuing repeat.
I’ve checked the belt tensions, and all seems okay.
Belt tension — the Z-axis should be guitar string tight (but careful not to bend the motor shaft): http://docs.carbide3d.com/assembly/shapeoko/xxl/step-5-belting/ on deep cuts it may help to remove one spring from the Z-axis temporarily, esp. if one hasn’t added a spoilboard on top of the wasteboard — it also helps to install the router as low as possible (installing the Makita adapter upside down will help). Some folks have found it helps to remove the M4 Z-axis tension bolt, apply a thin bead of threadlock along the length of the threads, then reinstalling it after it has dried.
This has happened to me, and it was the tension for the z belt. I thi k the clunk is it skipping on the belt. It felt tight (it would play a note if I plucked it) but I tightened it another 2 turns on the tensioner and was back in business.
Not sure exactly what you’re doing, but that “clunk” is the stepper skipping steps or skipping a tooth or more on the belt, and is why it’s “off” after that. What kind of cut? What plunge rate? What kind of tool?