There is a function in wp-markdown.php that determines if the prettify.js should be loaded:
/*
* Function to determine if prettify should be loaded
*/
function loadPrettify(){
$options = get_option($this->domain);
if(empty($options['prettify']))
return false;
$savedtypes = (array) $options['post_types'];
return is_singular($savedtypes);
}
This means that, on the main page of my blog, code will not be colorized. I recommend you change the final return to be:
return is_singular($savedtypes) || is_home() || is_front_page();