I know what you mean. The reason is that when zooming, the map has to be exactly centered on the poi, otherwise it would zoom in on the wrong location. If the map’s not tall enough, the infowindow may not be fully visible.
I’m not sure if it will help, but one workaround is to just make your map slightly taller so there’s room for the full infowindow.
I’ll see if there’s anything I can do in the plugin. I tried to center, zoom, and then open the infowindow, but then the map seems to jump around a lot, rather than having the effect of smoothly zooming on a point.
Google probably came to the same conclusion – maps.google.com works exactly the same way if you shrink the window a bit.