That's very interesting.
I certainly didn't change anything to do with the location of the .js files to make the galleries work--but it got me thinking.
I went back to the admin page, and tried to Preview the selected gallery. It doesn't work there either--at least there are no javascript functions available.
I wonder if it had anything to do with the upload of the redefined folder? Could the index.php file be calling for the javascript the wrong way based on folder location?
I looked at the index.php page, and here is the code that's there for the lines you showed above:
<?php } ?>
<style type="text/css" media="all">
@import url("<?php echo $pg_config['../Copy of ribbon_lightbox/path']; ?>css/slimbox/slimbox.css");
@import url("<?php echo $pg_config['../Copy of ribbon_lightbox/html_prefix']; ?>css/common.css");
@import url("<?php echo $pg_config['../Copy of ribbon_lightbox/html_prefix']; ?>css/<?php echo $pg_theme; ?>.css");
</style>
<?php if(empty($js_mootools)) { ?>
<script type="text/javascript" src="<?php echo $pg_config['../Copy of ribbon_lightbox/path']; ?>js/mootools-core.js"></script>
<script type="text/javascript" src="<?php echo $pg_config['../Copy of ribbon_lightbox/path']; ?>js/mootools-more.js"></script>
<?php $js_mootools = true; } ?>
<?php if(empty($js_slimbox)) { ?>
<script type="text/javascript" src="<?php echo $pg_config['../Copy of ribbon_lightbox/path']; ?>js/slimbox.js"></script>
<?php $js_slimbox = true; } ?>
<script type="text/javascript" src="<?php echo $pg_config['../Copy of ribbon_lightbox/html_prefix']; ?>js/gallery.js"></script>
The "Copy of ribbon_lightbox" looks like a result of duplicating the original ribbon_lightbox folder as per the instructions. I renamed it using the same instructions.