Hi and thank you for the great plug-in I understand it's a beta.the problem I'm having is with a multi-site installation using subdomains. The main site creates the site map at /public_html/wp-content/uploads/wpseo/sitemap.xml.gz
and Google webmaster tools I had to modify the robots.txt file to provide access to that location.
It also did not generate a robots.txt file
I have the plug-in enabled and all the subdomains with the site map feature disabled. if you can point me a be happy to report back anything I find.
I am at a loss on how to troubleshoot this and would be more than glad to give you access to the site