Guys i had the same problem and i found a way to fix that, you need to edit the main plugin file:
1- Go to the plugin page (plugins/jquery-lightbox-for-native-galleries) and edit jquery-lightbox-for-native-galleries.php
2- Search the line when the javascript start: // Output the Javascript to create the Lightbox
3- where says $(obj).find(“a”).colorbox… replace the “a” with “.gallery-item a”
4- where says $(“a.lightbox”).colorbox… replace the “a.lightbox” with “.gallery-item a.lightbox”
These steps will fix that problem, of course only telling a.lightbox will add to all links inside the gallery and that isnt useful if you are using another plugin with galleries like a paginator.
Please developers take note of this in future versions of this plugin.