I'm having an issue with generating a sitemap on a multisite installation. Since there's a workaround it's not a critical issue but in case anyone is having a similar issue maybe this might help troubleshoot.
One site is the root and the other is set as subdirectory. I have WordPress SEO active on both sites and have the settings set identically except for the name of the sitemap (sitemap.xml and sitemap2.xml). On both, the plugin reports that the XML Sitemap file is found and writable and that the URL is correct.
On the subdirectory site, clicking the Rebuild XML sitemap button results in the feedback report (eg. found, regenerated, updated, etc).
On the root site, clicking the Rebuild XML sitemap button doesn't do anything. I tried deleting the corresponding sitemap.xml file to see if the file was being generated and it was just a reporting issue, but the file isn't being generated.
BUT, if I edit a post on that site and republish, the XML sitemap is rebuilt automatically as it should be. So it's a simple enough workaround.
WordPress SEO 1.1. I don't have any other sitemap generating plugins active, although I used to use Google XML Sitemaps on the site where there are now issues.