do you do that by executing Font in each window? IIRC, acme tries to move the tag bar a line at a time, but does so using the sizes of your tag bar font (-f). you'll see this behavior occurs because the different heights on the fonts mean you can't satisfy both of them with whole-row-only moves. acme won't ever display part of a line of text.
doesn't address whether the gap should be black or not, but that's why it exists.