Not sure if you still need help but here is my 2 cents anyway. My cnc uses a small disc to set the zero or top of material. Whenever I changeout a bit or move the material around I need to re-zero otherwise things will not work out very well. I've had my CNC for about 4 months now and one of the very first things I had to do was flatten the surface. I'm not sure if you know what that is but it is a process where you create a rectangle the size of your maximum cutting area and use a large surfacing bit to peel off about 0.005 to 0.010" at a time. You may have to run this a few times to get the surface true with the cutter. Also the melamine layer is very thin probably only 0.002" which is not a lot. As a temporary test try using a thin spacer when setting your zero, this will fool the cutter.
This is all I have, hope it helps