That is because capo visibility is turned off by default (meaning it will not be applied when transposing chords). If you manually switch the capo value, it's going to flip it on (it's the little eye icon in the text display settings). There was a whole discussion about this on the forum, and the end result is that capo directives are honored in terms of populating the capo value and displaying them in the capo display, but they are not applied to chords unless you manually switch that on by tapping the eye icon.
Mike
Mike