xmlrpc.php should be passed through at WP::parse_request() at line 201

[toohokuaiki]

wp-includes/classes.php

// Don't try to match against AtomPub calls
if ( $req_uri == 'wp-app.php' )
    break;

AtomPub is through this foreach. XMLRPC also shuold be passed through. I think.

// Don't try to match against AtomPub calls
if ( $req_uri == 'wp-app.php' ||  $req_uri == 'xmlrpc.php'  )
    break;

I encount trouble when XMLRPC oparation below settings.
+ WordPress 2.9.2
+ ReWrite ON
+ WordPress url is ​http://example.com/foo/bar/some/path

[solarissmoke]

I might be wrong, but is this bit of code even loaded when pretty permalinks are enabled?

Server rewrite rules should mean that xmlrpc.php is executed directly. WP::parse_request() is only ever called from WP::main(), which is called from wp-blog-header.php, which is not included when you do a manual wp_load() as in xmlrpc.php.