If the option cache rebuild is checked, any POST request (this is most problematic because it includes wp-cron.php requests!) to any wordpress page/post will delete cached version of front page.
Workaround until bug is fixed:
Unchecking option cache rebuild.
Proposed bugfix:
Adding following code on line 58 of wp-cache-phase2.php:
if ( $_SERVER["REQUEST_METHOD"] == 'POST' ) {
wp_cache_debug( 'Supercache caching disabled. Only using wp-cache. POST request. ' . json_encode( $_POST ), 5 );
$super_cache_enabled = false;
}