If you're talking about Acrylics only, that results does sound really strange. When I was doing my test cutting of Acrylics, I didn't have any problems cutting the colors that would cut...some colors I could not cut, but those I could cut, cut cleanly. I was using my BenCutLaser CAM software. I have not cut Acrylic with it in a long time as I am focusing on the harder to cut 3mm woods, but I don't think I'd have any problems cutting Acrylics with it today.
If you're also talking about cutting woods, then you're running into the grain problem. Grain direction gives our low power lasers a special problem they have to deal with via CAM software. That's exactly why I created BenCutLaser, which deals nicely with that problem.