tsoares,
Juts to make sure we are on the right page. Everything worked on the dev subdomain but now trackbacks are not working for the production domain. The prodcution domain is a new site using MSM. You believe you have replicated everything.
http://blogs.cisco.com/ciscotalk/ is a site created using the multisite module.
ar is the blogname.There is a one index.php under ciscotalk directory.
Have you any settings in the path.php file in the ciscotalk directory that need to be updated for the blogs.cisco.com subdomain?
Have you added the $site_name variable to the path.php?