As of one week ago, my feeds stopped working, and I get Error: 404 not found errors on every possible feed address. Feedburner redirect plugin is turned off while I try to figure this out. I tried disabling all the plugins and re-testing the feed but that was not the problem.
The site: http://www.trueup.net
Host confirms that the .htaccess file looks fine.
I did upgrade to 3.1.2 recently, and recently added some custom post types and taxonomies and had some trouble with the permalinks for the taxonomy listing pages (all I had to do was visit the permalinks setting page and they were flushed & fixed).