I am using XCS because well it's easy for a beginner and I don't have to pay for it. Is there a way to adjust the focus height so the cuts are straight up and down.  I've tried manually telling the software the material is thicker than it actually is but that doesn't work.

When cutting 3mm plywood the bottom of the cut is nice and tight and the top has a lot more material taken out.  it's like the machine's focus point is the bottom of the material and not the middle for a more even cut.

It's very noticeable when doing layered designs, the bottom of the second layer over hangs the top of the first layer and so on.