I didn't check this over the weekend, so I'm a bit behind. When I suggested speed might be an issue I was inferring supper high feed rates. Such as greater than 1000ipm, obviously that isn't the case. Just wanted a reality check to make sure you weren't pushing the HSM limits of Linuxcnc.
I have seen very similar only larger marks caused by slop/backlash in an axis due to worn parts (bad bearings, worn out ball screw...) But that is on large wood routers, we'd never even notice marks that small. In our cases the backlash wasn't static, and couldn't be measured with an indicator in the usual way. It was more like the axis became soft and mushy and the backlash could only be measured under load. At rest or light load the axis would track correctly until you'd push on it. I think this is most likely either a mechanical or servo issue.