Thanks for the link! I tried that and it did help with the 404 error pages, but I’ve actually noticed something else.
With a non-default permalink structure, WordPress doesn’t just take over 404 error pages, but other error pages as well, like 500 Internal Server errors. This is really bad because with WordPress taking over errors, I can’t tell what’s going on when I have problems, since all I see is the good old “Sorry, no posts matched your criteria.”
I think this problem would go away if I installed my blog in a separate folder (not the root) and could store the .htaccess file in that folder, and not in the root of my domain. However, I want my blog to load on my home page so I don’t know any way around this. (I have my blog installed at /blog/ but I have WordPress loading it at root level. So I have index.php and .htaccess copied to my root directory. I think that’s what’s causing problems.)
