I realized that I was accounting for the kerf of the laser cutter, or the amount of material removed during the cut. While the laser cutter removes little material during cutting, nevertheless, it still removes some, enough to affect the tightness of joints. How I measure the kerf is draw a 100mm by 100mm square in Lightburn and then cut it out of the material I am working with. The kerf will be different for different materials.Then after the cut measure the dimensions of the cut square with calipers. The square will be slightly smaller than the 100mm drawn. The difference is the kerf. In this case, the kerf for 5mm thick plywood is 0.26 mm.