I just downloaded the latest version of the Whispy theme and I can confirm this problem.
Here is the solution (for the homepage only!).
in the directory wp-content/themes/whispy, find and open the file page.php. Add the following code directly after the php opening tag '<?php':
$whispyOptions = get_option('whispy_theme_settings' );
if( $whispyOptions['colspost-index'] == '3' && is_front_page() ) get_template_part( 'threecolumn-page' );
Now, in the same file, add directly after the php closing tag '?>' the following code:
Safe the file and your homepage should show 3 columns when this is set in the theme options. Cheers!