My first suggestion would be to switch to the default theme and see if it still happens. If it doesn’t happen with the default theme, then it’s a bug in your theme.
A common cause of pull-quotes occurring twice is buggy themes that call the wp-head stuff twice. It should only be called once.
As for appearing over the header, this could be a nesting issue, again with the theme. Make sure the <span> is located inside a paragraph and see if that fixes it. In terms of HTML, the pull-quotes appear at the top of the Parent of the <span>. Thus if the span is inside a paragraph, the quote should be at the top of the paragraph.
