Watermark is part of an image, so there’s no place for conflicts with any lightbox scripts. It could happen though in a situation when lightbox effect uses image size (full, large, custom or any other) that is not selected in “Apply watermak for” option in WI settings page.
In other words if you don’t apply watermark to image size used by lightbox for large version of images, it won’t be visible (because it’s not there).