Omtech 100W Laser here. Cutting plywood (3mm) I get dark lines on the cut. On the back of the wood you can also see several burnt spots. What is the reason for this, is there any way to improve this? Omtech suggested to try upgrading the motherboard firmware, which I would like to avoid as otherwise the machine is working fine. Thank you.
Those look very much like scorches reflected from the honeycomb platform.
You may have better results putting the material on the knife-edge bars, although they will also produce small scorches where the beam bounces off the metal.
With a bit more forethought, you can raise the material on spikes and let the cutouts drop to the platform:
With either of those, the cutouts must fall cleanly, because when one part sticks another part will inevitably rise to collide with the laser head on the next pass. 
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