Draftboard can swell with humidity over time and warp slightly too. Make sure the material is perfectly flat (it always helps to pin the material flat with the Honeycomb Pins), clean the lens in the head (which you said you did), and if you still have issues, measure the actual thickness of the draftboard in several places with a good digital caliper. If it’s significantly thicker than 0.125", then it has swollen a little and you might need to reduce the cutting speed by about 5 or 10 points to get complete cut through in one pass.
All of my draftboard swells to from 0.134-0.146" and I usually have to run things a little slower to compensate for it. (Very humid here.)