Brian at VaultPress showed my that all it takes is adding one line to your wp-config.php file to make everything work.
* For compatibility with CloudFlare
if ( !empty( $_SERVER['HTTP_X_FORWARDED_FOR'] ) )
$_SERVER['REMOTE_ADDR'] = $_SERVER['HTTP_X_FORWARDED_FOR'];
CloudFlare and VaultPress now play quite well together. We have noticed many of our pages are loading a good deal faster, and domain name resolution happens in a flash.