Mmm, I think I see what's happening now. A familiar only appears in one place no matter what — in the favorite/recent list or in the full hierarchy or currently active. Appearing in any of those places removes it from all the others, which was confusing me; I was expecting the hierarchy to be a complete list of owned familiars at all times. Come to that, I suppose I also expected the recent/favorite list not to change when one of those was made active either. And then, of course, selecting the already-active familiar from somewhere would do nothing.
The way this works seems to violate some kind of principle of UI design, though I couldn't tell you which one that would be, off the top of my head. I feel like selecting something should place a checkmark next to it, not remove it.