zigmeister, help me out here.

I am pretty certain your saddle height is the same. That should be a given. You mention that your reach is near identical and you talk about stems, but not about the effective top tube length, head tube height, or any other frame geometry.

Why do you have a lower slung position now? I think the answer is somewhat obvious, your bars are lower and you have more bar-to-saddle drop. Couldn't you have done this on the previous size 56 frame with the right combination of stem and spacers? (Should be a "yes" unless running a slammed -17 stem on the 54.)