As a guess, I’ll bet you are taking your home Z position from the top of the stock and its height off the spoil board does not match the one you have in your authoring software. And this kind of error can be doubled when doing two-sided milling. As a start, home your bits against the spoil board, move up the thickness you have for your stock in your authoring program, then zero your Z again. This will assure that your Z height off the spoil board matches what you have authored.