Same kinda problem as the people above. Some background:
I use http://www.xml-sitemaps.com/standalone-google-sitemap-generator.html because some of the pages I want on the sitemap are not produced by wordpress.
What is so very annoying is that the wordpress seo plugin moves the sitemap.xml / sitemap.xml.gz (generated by another plugin) from the root to wp-content/uploads/wpseo. All of this even though I have “Check this box to enable XML sitemap functionality” in the wordpress seo plugin unchecked.
It took me a few days and some head scratching to figure out why my sitemap kept disappearing 🙂
