I just renamed the htaccess and it did fix the problem however I am not sure what needs to be edited. Here is the file:

# -FrontPage-

IndexIgnore .htaccess */.??* *~ *# */HEADER* */README* */_vti*

<Limit GET POST>
order deny,allow
deny from all
allow from all
</Limit>
<Limit PUT DELETE>
order deny,allow
deny from all
</Limit>
AuthName edited.com
AuthUserFile /home2/edited.pwd
AuthGroupFile /home2/edited.grp

<Files *.ss>
Order deny,allow
Deny from all
Allow from 127.0.0
</Files>

<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /

RewriteCond %{REQUEST_URI} !(\.gif$)|(\.jpg$)|(\.png$)|(\.css$)|(\.js$) 

RewriteCond %{REQUEST_URI} ^(.*)$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule .* sapphire/main.php?url=%1&%{QUERY_STRING} [L]
</IfModule>

John,
By default Silverstripe grabs all incoming requests and interprets them as requests for Silverstripe pages. To get it to ignore the requests for your sub-folder, you need to modify the .htaccess file at the root level of your site. Add the following line:

RewriteCond %{REQUEST_URI} !/whmcs/ [NC]
immediately after the following line:
RewriteCond %{REQUEST_URI} !(\.gif)|(\.jpg)|(\.png)|(\.css)|(\.js)|(\.php)$

Let me know how it goes.

That fixed it. Thanks!