Following the exceedingly simple method from Andralor here fixed the issue for me: https://github.com/fancyapps/fancyBox/issues/766
Essentially, call the iframe again onUpdate:
$('a.js-fancybox-iframe').fancybox({
type: 'iframe',
scrolling : 'visible',
autoHeight: true,
onUpdate: function(){
$("iframe.fancybox-iframe");
}
});