Chances are that its a feature or function of the theme you are using. That theme designer from Theme Forest is very good and it wouldn't surprise me if that is where it is coming from. These days, many premium themes come with lightbox systems built in. I've had the two stacked lightbox issue before with one of the plugins I use with my theme. Sounds like you don't need a lightbox plugin at all.
However, if you feel that the plugins give you better control over the lightboxes and you prefer to handle it via plugin, see about disabling them in the theme. Check the theme's settings and admin pages for lightbox setting, if there isn't anything, check with the theme developer to learn how to deactivate it (the best method for deactivation would be a define statement in wp-config since this would make it upgrade friendly).