WordPress making other files 404

After I installed wordpress on my site, freedomdown.net. I have started getting 404s when the file is really there if non-wp files.

For example:
http://www.freedomdown.net/fd/anonymail.php
gets a 404.
But now go to:
http://www.freedomdown.net/fd/
And you will see that yes, this file really is there and should load.
That file was there before wp was installed, and loaded fine.

I have an odd feeling it may having something to do with the htaccess, but I really do not know.

Please help,
– Erik