I’m wondering…
I just upgraded from 2.0.3 to 2.0.4 before I turned on the pretty permalinks (I’m in the final stages of switching the site over to WP).
I have another site that’s still on 2.0.3, and it works fine, but has a blog name in it, like this:
mydomain.com/BLOGNAME/the-permalinks
And it doesn’t insert index.php in there. Could it be something in the upgrade, because otherwise, the server is the same.
I really want the security upgrades of the latest version, but I’m wondering if it’s the upgrade?