After upgrading from 2.9.3 (I think) two things happened. First, all permalinks to categories and tags died, and second, all category rss feeds came out without any items, only channel info is available. Getting this on two blogs, both installed in a subdirectory.
I managed to find a temporary fix using the plugin WCS Custom Permalinks Hotfix http://wpcodesnippets.info/blog/wcs-custom-permalinks-hotfix.html but I would rather have a more permanent solution that lets me have permalinks AND working feeds + category/tag pages.
Ps: Yes, I have tried to follow numerous threads and tutorials on how to fix this problem, for example rebuilding the htaccess, testing with another theme, switching off all plugins, etc etc, but nothing seem to work. And no, I'm not using Advanced Permalinks or Simple Tags.
Can this please be elevated to a formal bug in wp 3.x.x ?
Update: Oh,it has been written up as a bug, but still no solution? http://core.trac.wordpress.org/ticket/16662