Tried that also, it must have been a filter problem, an IT guy at the office added this code to the plugin and now the links work again.
<div class="mslide mslide-<?php echo $meteor_count; ?>">
<?php // Adds slide image with Slide URL link
if ( get_post_meta( $post->ID, "slide_url_value", $single = true ) != "" ): ?>
<a>ID, "slide_url_value", $single = true ); ?>" title="<?php the_title(); ?>">
<?php $src = wp_get_attachment_image_src( get_post_thumbnail_id($post->ID), 'featured-slide', false, '' );?>
<img width="<?php echo $src[1];?>" height="<?php echo $src[2];?>" class="attachment-featured-slide wp-post-image" src="<?php echo $src[0];?>" title="<?php the_title(); ?>" /></a>
<?php // Adds slide image without Slide URL link
else: ?>
<?php the_post_thumbnail( 'featured-slide', array( 'title' => get_the_title() ) ); ?>
<?php endif; ?>
</div><!-- .mslide -->
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