Could it be that you are adjusting one carburetor and reading the vacuum off of another? I ask because cylinders 1 and 2 are synchronized together, as are cylinders 3 and 4. When I balanced the carbs on a 400 using a manometer, I noticed that as I raised a slide (lowering manifold vacuum), the adjacent carburetor indicated a vacuum increase.
Once #1 matches #2 and #3 matches #4, you have to get the two sets to match each other. Patience helps.
Bob