You could try removing everything in your home.php file right after this code –
// Home Bottom Message
add_action('genesis_after_content', 'agile_bottom_widget');
function agile_bottom_widget() {
if ( is_active_sidebar( 'bottom-message' ) ) {
echo '<div class="bottom-message-wrap"><div class="bottom-message-inner">';
dynamic_sidebar( 'bottom-message' );
echo '</div><!-- end .bottom-message-wrap --></div><!-- end .bottom-message-inner -->';
}
}
Everything above that code is the code for your widgets, so leave that as it is.
Make sure and leave the genesis();
line at the bottom….and see if that works.