Yesterday, I’ve released version 0.97 of Folder Gallery. The main changes are related to the lightbox JS engine.
A last option (“None”) removes all lightbox script from the galleries generated by Folder Gallery. That way, you can use another plug-in to display the gallery pictures. This works with many lightbox plugin including Fancybox 1.0.7+ by Kevin Sylvestre, jQuery Colorbox 4.5+ by Arne Franken, Lightview Plus 3.1.3+ by Puzich.
You can get Folder Gallery at wordpress.org.