John,
As I recall your back material is applied to the the back of the cabinet, though inset in a rabbet (full dado). As Gary indicated, you should use a 3/8" material instead of 1/4" when you design the cabinet. Since you're using 3/8" in your design, the resulting full dado or rabbet will be 3/8". If you use 1/2" material, it'll be 1/2". The machine does not know what material you layout on the table, so when it comes time to cut the backs, you just put a 1/4" on the table instead of 3/8".
If you'll recall, I suggested that you should create a material and name it so that you know to load 1/4" material instead of the 3/8" or 1/2", that we discussed. Since the material has a different name, it will nest all the parts made with the same named material.
With regards to setting up zero. If there are no dados or other joinery in the back, then setting up z-zero to the table surface is not necessary. They are all thru-cuts, so the retracted height is a little higher than necessary, but that's okay. It's not deeper!
You've probably already figured this out, but if not.
Happy New Year to all,
Dennis L. Englert