There could be a minor difference between the 52 and 54...

The 54 is likely to have a slightly longer head tube than the 52, so you will sit a little more upright assuming the same saddle position and crank length.

You can adjust the handlebar height to be the same as a 52 by removing a spacer or two, or by switching stems on the 54... This could give you the same riding position with your preferred top tube length.

The difference you are feeling could theoretically be partly based on the shorter top tube as well.