Pocket clearing vs finish height

While creating a pocket, the finial pass with a small bit is a different height than the clearing pass. I have a 1m xcarve, Vcarve desktop and a 3 axis zero block. Before I had the block, it assumed I was just off on my zeroing. but after adding the block, and verifying that the zero is in the correct place across multiple bits, the problem is still there. it seems to be even around the whole project, and looks like a trough around the edge. It has persisted with all pockets. Normally, I’m ok with it because I normally fill the pockets with colored resin. Am I missing a setting or something? The difference is a little over .02".

Vcarve Desktop. Not quite the right wording on it, I mean the larger clearing pass vs the small bit that finished the pocket. I use a 1/8 for clearing the large portions then run a 1/32 for detail. The small bit cuts deeper than the large bit. Both paths are created together.
I have calibrated the whole machine.

How do you do that?