Why does Nextgen change my Footer?

I’ve got an Artisteer based theme with a UberMenu menu and Nextgen Gallery (nothing else, not even Akismet or Hello Dolly).

But when I activate Nextgen, my footer gets messed up.

This is my PHP:

<div id="wp-footer">
	<?php wp_footer(); ?>
	<!-- <?php printf(__('%d queries. %s seconds.', THEME_NS), get_num_queries(), timer_stop(0, 3)); ?> -->
</div>

<!--This stays at the bottom-->
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js" charset="utf-8"></script>
<script type="text/javascript" src="<?php bloginfo('template_url'); ?>/nagging-menu.js" charset="utf-8"></script>
</body>
</html>

You would expect then everything under <!–This stays at the bottom–> can’t be altered, because these is nothing underneath that line that refers to wp_footer.

However, this is my footer without Nextgen turned on:

<div id="wp-footer">
	<script type='text/javascript' src='http://www.mijncreaties.com/opstal-testsite/wp-content/plugins/ubermenu/core/js/hoverIntent.js?ver=3.8'></script>
<script type='text/javascript'>
/* <![CDATA[ */
var uberMenuSettings = {"speed":"300","trigger":"hoverIntent","orientation":"horizontal","transition":"slide","hoverInterval":"20","hoverTimeout":"400","removeConflicts":"on","autoAlign":"off","noconflict":"off","fullWidthSubs":"off","androidClick":"off","iOScloseButton":"off","loadGoogleMaps":"off","repositionOnLoad":"off"};
/* ]]> */
</script>
<script type='text/javascript' src='http://www.mijncreaties.com/opstal-testsite/wp-content/plugins/ubermenu/core/js/ubermenu.min.js?ver=3.8'></script>
	<!-- 33 queries. 0,480 seconds. -->
</div>

<!--This stays at the bottom-->
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js" charset="utf-8"></script>
<script type="text/javascript" src="http://www.mijncreaties.com/opstal-testsite/wp-content/themes/vanopstal/nagging-menu.js" charset="utf-8"></script>
</body>
</html>

And this is the footer with Nextgen turned on:

<div id="wp-footer">
		<!-- 37 queries. 0,664 seconds. -->
</div>

<!--This stays at the bottom-->
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js" charset="utf-8"></script>
<script type="text/javascript" src="http://www.mijncreaties.com/opstal-testsite/wp-content/themes/vanopstal/nagging-menu.js" charset="utf-8"></script>
<script type='text/javascript' src='http://www.mijncreaties.com/opstal-testsite/wp-content/plugins/ubermenu/core/js/hoverIntent.js?ver=3.8'></script>
<script type='text/javascript'>
/* <![CDATA[ */
var uberMenuSettings = {"speed":"300","trigger":"hoverIntent","orientation":"horizontal","transition":"slide","hoverInterval":"20","hoverTimeout":"400","removeConflicts":"on","autoAlign":"off","noconflict":"off","fullWidthSubs":"off","androidClick":"off","iOScloseButton":"off","loadGoogleMaps":"off","repositionOnLoad":"off"};
/* ]]> */
</script>
<script type='text/javascript' src='http://www.mijncreaties.com/opstal-testsite/wp-content/plugins/ubermenu/core/js/ubermenu.min.js?ver=3.8'></script>
</body>
</html>

Thanks to this behavior, Nextgen interferes with the performance of the UberMenu menu. And since this is a very important part of the design, I can’t use the website without this performance.

On the other side, I really wonder why and how Nextgen can put any lines of code in a spot where there is no call to wp_footer or something like it. Is it because Nextgen is really agressive? Focring lines of codes where they shouldn’t be?

But most importantly: what can I do about this? How can I fix this.
I enjoy using Nextgen, but right now it’s killing my website.

For the record, I’m using the latest version (just installed it fresh) Nextgen, and latest version WP.

http://wordpress.org/plugins/nextgen-gallery/