The latest version of PrettyLink is not compatible with the recent changes in WP3.5 with the XMLRPC.
I had to go in prli-xmlrpc.php and comment out all the checks for the enable_xmlrpc flag in order to be able to use the API of my blog.
If there is a better way, then please let me know.
if ( !get_option( 'enable_xmlrpc' ) )
return new IXR_Error( 401, __( 'Sorry, XML-RPC Not enabled for this website' , 'pretty-link') );
I tried adding enable_xmlrpc in the options table and that didn't work, id rather change the code of a plugin that mess with WP settings anyway.