Subdirectories Showing Internal Server Error, WordPress in Root

I had recently helped a client install WordPress onto his root directory. However, he says when it was installed, he stopped getting crawl results for the sites in his subdirectories. Those sites are straight HTML/CSS–no WordPress–and have domains pointed to them. When I try to load non-existent pages in those subdirectories, I get an Internal Server Error (instead of a 404).

The .htaccess file is the usual WordPress one (probably replacing what was once there):

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php
</IfModule>
# END WordPress

The closest thread related to my problem is here: http://stackoverflow.com/questions/8358044/internal-server-error-in-subdomains, but it offers no solution. Is there one at all?

I have never worked with the .htaccess file before, so any help/explanation is appreciated!