Several things can cause an incomplete cut, some of the most common are:
- Material that is not perfectly flat on the tray. If you aren’t using something like the Honeycomb pins or strong SHIELDED magnets, the odds are very good that the smallest amount of warp in the material can keep it from cutting through in places.
- Dirty optics. (Sounds like you cleaned those, if you make sure you cleaned the two small windows on the bottom of the Print Head, along with the lens inside, the window on the side of the Print Head and the hidden window on the left side of the laser arm, it probably isn’t that.)
- The material itself. Cheaper plywoods purchased locally can have air pockets, knots, glue plugs and worse…and those spots and patches are not laserable. The laser will just char the dickens out of it and not even make it part way through. Different material might work better for you in that case.
- Having the wrong settings for whatever you are trying to cut.
Any of the above can cause incomplete cuts. In some cases, you can try to finish a cut by sending a second pass without moving the backing material or changing the screen alignment. Test to see if a cut is complete by holding down the backing material and trying to lift the cutouts with tape or a pick.