Given details in the question, I assume you're using 4.0.xx. I see the same thing. I hadn't noticed this but I don't really use stack/reach.

There is an intended workflow in 4.0 it seems. Enter Fit information in the Fitting Tab. Then go to the Geometry tab and click 'Import fit information' under the Geometry tab. Input the geometry details. I generally click the Update Canvas button when changing tabs - I'm superstitious. Next move on to the frame & Frame Tubes tab and enter details there. Once you change the headtube length, the stack changes but the prior tab doesn't appear to have that information so, you have to go back to the Geometry tab and 'Import Frame' if you want them to match. You'll get a little popup and some prompts but this will back populate the tube details to the Geometry tab. Once I did that, the stacks matched.

I may open up a prior design file and compare to my printouts as I change different things just understand the new version better. Manfred has been super responsive when I have asked questions as well.