I have experienced this terrible noise too. The head seemed to find the snapmarks, then went to the left and made this terrible noise and the snapmark canceled itself. I was able unfortunately to repeat the failure several times. Tech support pointed me to this forum.
I have used the snapmark successfully before on other projects, but I have not found a fix for this. The ruler was laying on top of a 1/4 inch plywood (free snap ruler design here).
Some thoughts are maybe it is messing up because I’m telling the thickness to be 1/4 inch, but laying the ruler on top increasing the thickness and messing up the “ideal” snapmark image the machine is focusing in on. Or maybe the strong magnets are messing up the head when it passes by. Or maybe this is why it is still in beta… I dunno.