As per the pinning option that you have selected it maintains this distance from top and middle of the browser window,
So, that explains why the on reducing the width or the height of the browser the logo goes beyond the page or footer respectively.
At this point you can't restrict the pinned object to stop at a particular location, I would appreciate if you can add that to the ideas section over here, http://forums.adobe.com/community/muse/ideas
Done and done, I've added the issue/idea in the link you sent me. Here's hoping that this function will be seen in future updates of Muse.