The problem with z-index is that it is relative. By moving the div so it's a child of the body tag, it will have a relative z-index to elements that are also children of the body tag and not of the body tag's siblings' children.

See http://stackoverflow.com/a/7482870 for a good explanation.

I managed to get it working by overrridng the bPopup "append" function (with a handy parameter), and using JQuery clone() and remove().