My theme uses fancybox also, and I can’t rebuild my theme around Instapress. Here’s how I resolved my issue with Fancybox not working:
Disabled effects, yet still used effect=”fancybox” in the shortcode.
– It links the thumbnail to the image, not to the Instagram page of the image.
Used my theme’s Fancybox instance.
– added the ff. javascript somewhere in the footer:
<script>
jQuery(document).ready(function($) {
$(".instapress-shortcode a[rel=instagram-sc-images]").fancybox();
</script>
Hope this helps.