Hey stypaldos!
I'm not really sure what you mean. With galleries do you mean slideshows/carousels with the carousel addon? http://laytheme.com/carousel.html
Or do you mean that you have sections of images where you want the lightbox to only work for a certain section.
Do you have a link?
It's not exactly what you want I think but maybe that could be a solution to use this setting:
In "Lay Options" -> "Lightbox Addon" -> "Only Zoom"
This way you can't slide to next/prev images at all but you can only enlarge an image and close it again.