James-
Are the toe kick materials set up correctly in the materials build assembly ? In CV ?
We use different sizes. 6 5/8 for the stretcher and 5" for the nailer and 4" for the toe kick.
Tool table and spoil board cut. This is our experience with CV and Biesse. We flycut the spoilboard with a predetermined key on the controller with a given number like 18.5 and tell it we want it @ 18.25 and run the flycut at "O" which that key told the machine was the new zero, but in reality the flycutter will make it to 18.25. Then we will check the depth of the cut by the tool we change only when we change them out in the tool holder, (only once when we change out the cutters) in relation to the depth in the spoil board and enter the correction in the tool table. You should not have to fool with any settings in height once you measurements and tests are where you want to be.
I would venture to say you need to look @ your s2m printouts and count your parts. Once code is generated, I find it hard to assume the editor/controller @ the router would add or subtract parts. And we run a shit load parts
I hope this helps