Z Depth incorrect after tool change

Started making my first project that involve a tool change. Everything works great as far as the stopping of the tool and the homing procedure however after the tool change and the z-home it appears the next tool is about 2mm off from the depth of the first one.
For example I did a project where I used a 1/4" 2 flute to do a 2d pocket to clear away the majority of material, then changed tools to an 1/8th 2 flute for a contour to clean up the rest of material and add some detail, It ended up that the 1/8th" mill was about 2mm higher than the 1/4" Mill. Which made a shadow along the profile. After the contour I changed tools again to a 90 degree chamfer for some engraving and that was the same thing. It ended up being about 2mm too high which screwed up the depth of the engraving.
I am using fusion360 for everything, The post processor recommended on the milling basics page, then using CNCjs to send it to the SKR Pro 1.2 board. I am also using the z probe and have configure the zplate thickness in the post processor. It almost seems like there is a 2mm z offset somewhere in the code or in fusion somewhere that I can’t find.
Stock dimensions are fixed and accurate. I also Probe Z on job start to make sure I am right on at the start of the job.

Check the ‘roughing depth’ or something like that. It sounds like you have a ‘leave behind’ set to 2mm on the second two processes. There’s two different types of ‘leave behind’ one is radial and the other is (something I can never remember). If I remember correctly, radial is the xy and the other one is z.

I think your talking about the “stock to leave” option. I thought of that because when i made the 2d pocket with 1/4" mill I turned on stock to leave and set the radial stock to leave at 1/16" so that I could go back and clean up with the 1/8" mill. but didn’t realize that it had defaulted the axial stock to leave at 1/8" as well… so because the model is only 1/8’ deep it would just touch the surface and move on. I had to set the Axial stock to leave to 0 so that it would mill down to model bottom. See Pic

But on the 2D contour for the 1/8" mill I don’t have any roughing passes or stock to leave turned on.

Could it be that the contour likes the bottom of the pocket geometry to be selected rather than the top? it shows the same preview either/or
Everything in Fusion looks perfect as far as preview and simulation.

That’s very possible.

I usually pick the bottom when I do a pocket, so I didn’t think about that.

On the pocket I selected the bottom geometry but for some reason on the contour it would let me select the whole outline if the bottom of the pocket. It broke it up into a bazillion lines that would have to select. Some pockets worked fine and let me select the bottom and some wouldn’t…it was wierd.