I had the same issue, I edited the plugin file directly to fix it.
lightbox-gallery.php
Look for the function lightbox_gallery($attr), a little ways down make the code resemble this. All linked images will be the size you set here, thumbnails will remain thumbnails.
/*if ( !empty($options['global_settings']['lightbox_gallery_lightboxsize']) ) $lightboxsize = $options['global_settings']['lightbox_gallery_lightboxsize'];
else $lightboxsize = 'medium';*/ $lightboxsize = 'large';