We have a WP multisite install 3.9.1 subdomains not directories. When a user is in the main site or network admin (ie. the URL is the primary domain), logout works fine.
sites.ucsc.edu is the primary domain.
When a user tries to logout from a subdomain like gildas.sites.ucsc.edu, it appears to log them out but if they try to go to the dashboard, they are still logged in.