I spent the better part of a Friday night sorting this out. I had just launched 4 new wordpress blogs that were secondary installs on each server. (I use a VPS and /home/domain/www/ was the primary wordpress install – the secondary installs existed at /home/domain/www/secondsite ) . The problem was that I switched on the fancy permalinks in the control panel of wordpress and after that nothing worked but the main page. Setting things back to the default I could see posts, but not the feed or anything else that relied on mod_rewrite.