Top directories can break functionality on sub directories. Case in point:

Scenario: WordPress site with popular application, helpdesk.
http://www.qualityunit.com/liveagent/

some_site.com

Generally the root level htaccess file of WordPress contains a statement:
“RewriteBase /”

This causes the following example URL to break:
some_site.com/helpdesk

You need to create a new statement in the /helpdesk directory folder’s htaccess file:
RewriteBase /helpdesk/

This applies to any other application that may reside in sub directories.

Enjoy!

Keywords: Rewrite, wordpress,  base, directories