In AF-S, the aperture stops down after acquiring focus wide open. It all happens rather quickly. As soon as the focus square turns green, the aperture stops down (presumably to give depth of field preview? although, it does this even with "preview pic effect" off, which doesn't make much sense). But it's actually doing the focusing with the lens wide open. Try focusing on something with low contrast that takes longer to get a lock on. You can hear the aperture click on some of the lenses and also you can see the difference in depth of field in the preview.
In AF-C, the aperture is stopped down the entire time the camera is focusing, which is really pretty daft and makes one question the competence of the Fuji engineers. I mean, I'm in single shot drive mode here, so it's not like I even need an aperture mechanism that can open and close at 11 FPS.
Hopefully it's just a bug, but I'm not comfortable gambling $1600 on them deciding to fix this (and many other issues) in a future firmware update... I'll just re-buy the camera then (when it's hopefully cheaper and fully functional).