This is all due to your .htaccess files and RewriteEngine rules.
In any subfolder of the site you DO NOT want to get redirected back to the bootstrap (index.php) and thus pushed through the MVC you need a new .htaccess with the following:
ie. in htdocs/forum you need this .htaccess
As for the sites you have living under the web root htdocs/site1, htdocs/site2, etc. you need to set the Base Path for the RewriteEngine so its looking in the correct location. For more details and help with mod_rewrite check out the
Apache Docs