Oh yeah, the cutting problem is common…everyone expects the materials to be completely uniform, but they’re not. Things like humidity can swell them, the slightest amount of warp will affect it adversely (as little as 1 mm), so what most of us do, especially if we live in a humid area, is to use pins to flatten out the boards on the bed, and sometimes, we send a second pass, or slow down the cutting speed by about 5 to 10 points. Any of those will work to give you better results.
Cut yourself a few of these honeycomb pins…they are a lifesaver. And if the cut doesn’t make it all the way through, you can just send the cut again as long as you do not move the material on the bed or the image on the screen between cuts. (Just use a piece of tape to pull up on the cutout to see if it is clear before taking the material off of the bed.)