I have the same situation as described here: http://mu.wordpress.org/forums/topic/18172
XMLRPC publishing on my main WP MU blog is working, but on the subdomain isn't...
One and a half yea ago I fixed this problem by adding subdomains to /ect/hosts file on my web server, see http://developernote.com/2012/01/getting-wordpress-multisite-work-with-windows-live-writer/ for more information.
But it stopped working again and this workaround does not help anymore.
What can cause this situation to occur? Is there some bug or I am doing something not quite right? I have WordPress MU Domain Mapping plugin installed on my WP, probably it affects XMLRPC functionality somehow?