I have just come up with a similar issue and fixed it by adding the following to the end of the links: <?php echo the_ID(); ?>
The fancybox link has the following:
<a class="fancybox" href="#inline<?php echo the_ID(); ?>" title="<?php the_title(); ?>">
The lightbox information has the following:
<div id="inline<?php echo the_ID(); ?>" style="width:360px;display: none;">
Hope that helps someone
