EDIT
Try this code:
remove_action( 'genesis_loop', 'genesis_do_loop' );
add_action( 'genesis_loop', 'sk_do_loop' );
function sk_do_loop(){
global $wp_query;
$temp_query = $wp_query;
// Fix for the WordPress 3.0 "paged" bug.
$paged = 1;
if ( get_query_var( 'paged' ) ) { $paged = get_query_var( 'paged' ); }
if ( get_query_var( 'page' ) ) { $paged = get_query_var( 'page' ); }
$paged = intval( $paged );
$args_spotlight_latest = array('posts_per_page' => 5,'post_type' => 'spotlight', 'post_status'=>'publish','meta_key' => 'featured_slider','meta_value' => 'true', 'paged' => $paged);
$spotlight_posts_latest = new WP_Query($args_spotlight_latest);
$wp_query = $spotlight_posts_latest;
/** Content Area **/
if($spotlight_posts_latest->have_posts()){
while($spotlight_posts_latest->have_posts()){
$spotlight_posts_latest->the_post();
$feat_image = wp_get_attachment_url(get_post_thumbnail_id());
..............
..............
..............
}
}
genesis_posts_nav();
wp_reset_query();
}