I use this:
1. in Settings-> FancyBox for WP-> Galleries tab select “Use a custom expression to apply FancyBox”
2. delete java auto-apply snippet (all content in the text box)
3. now you MUST add ‘class=”fancybox”‘ to any element you want to apply fancybox to.
4. alternatively write a java snippet to auto apply class=”fancybox” to selected elements automatically