This is all very strange.
If my main index page is called anything other than "index.php" (I changed it to "index3.php" for testing), then that page gets a 404, but all the links work just fine, even though I've set WP to look for "index3.php" as the main page ("Options >> General >> Blog Address").
My Blog Address is set to "index3.php." Check it out:
http://www.nextvista.org/index.php/
http://www.nextvista.org/index3.php/
Though I've told WP to look for "index3.php," "index3.php" returns 404 while "index.php" works just fine.
And it's just the home page ("index3.php") page that doesn't display properly. From that "index3.php" page (the one that returns 404), if you click on the December archives, this is what you get:
http://www.nextvista.org/index3.php/2005/12/
Notice the permalink structure; that's what I want. I don't see why the name of the index page would have anything to do with whether or not the permalinks work.
If I change the permalink structure back to "default" via the dashboard, everything is fine and operational (but the permalinks are not very user friendly).
Side Note
In case it's important, no matter how I alter the permalink settings in the dashboard, here are the .htaccess rules I am told to create:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /index3.php/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index3.php/index.php
</IfModule>
No matter the permalink structure, those are the rules. Shouldn't those rules change if I change the structure? Maybe that's a different issue, but I thought I'd throw it out there in case WP is telling me the wrong rules to put into .htaccess. If this is unrelated, ignore it and I'll ask it later.