I just tried writing a new post, and it doesn’t show up (I get the host company’s 404). All my content is pages, not posts – I link to the pages in a blogroll on the front page. I don’t know if that info is helpful.
I was playing around with some files and now the home page is index.php in the root directory. That seems to be the only way to get the front page to work. I deactivated the filosofo to see what would happen and the permalinks are still doing the same thing.
Thanks! I had just finished figuring that out. I had never been inside the database like that before, so it was scary. Good to know that my instincts were right!