Okay, so it's actually working as designed. That option sets the Maximum popup size, not the preferred size. When building the popups it tries to make them "square-ish" while guaranteeing that the popups will never be taller than the Max Popup Height. It trades accuracy for speed, so the results are sometimes a little off.
I'll look into how much work it would be to add a config option to make it work more like you were expecting.