You two are on the right track - there are two variables at play here, and without some prior exposure to CNC, it would be hard to guess what they are let alone make plans to correct them.
The bed itself is a fixed piece of the machine that has no adjustment. We’ll want to leave that alone.
Variable #1 - Uneven wasteboard. This is an easy fix, and @zmocar came up with the correct answer: You need to surface the wasteboard so it is true to your spindle. Taking 1mm off the entire board (assuming the lowest point isn’t more than 1mm) will achieve the desired results. You may even be able to begin by taking 0.5mm away. This is a common thing that needs to be done on all CNC machines. You don’t need to do it all the time, but anytime you install a new wasteboard, OR your wasteboard becomes too scarred up, you’ll need to run a surfacing operation.
Variable #2 - Uneven material. Chances are really good that the material you are cutting isn’t perfectly flat. In fact, if you took a reading across the material you will probably find at least a couple thou of difference from one side to the other. You have two choices
1.) If the material is something you’re engraving (i.e. you want to save the top of the piece)- you can figure out a way to shim it (from the bottom) so it’s even. This isn’t all the common of a practice, but in some cases can be done. Or, you can flip the material over and surface the face you’re not concerned about keeping.
2.) Just like in Variable #1, you can surface the material you’re going to be cutting from. Standard practice would be to use a material that’s slightly thicker than your design calls for. After you’ve loaded the design into meshcam, you can set the ‘extra’ material to be on top of the z. Then, by default, meshcam will mill that material away before it begins cutting your actual design.
-Edward