The usual suspect is the flattness of the wastboard. If you are sure it is flat then the next in line are the mechanicals. Check your v-wheels and belt tension. Belts are not likely but they can contribute. Next mark your bit in the collet. The bit could be slightly loose and moving up and down. If possible run a surfacing pass on your material… Attached is a document about checking your v-wheels and flattening your waste board.
spoilboard_considerations.pdf (1.3 MB)
homing_problems.pdf (1.2 MB)
Both of these documents mention flattening and v-wheel adjustments. I have a stiff nylon brush I clean my v-wheels with. I power off the Shapeoko and move each axis back and forth and clean the v-wheels. Additionally I use a 3M finishing nonwoven pad (white) to clean my rails, not sandpaper.