My situation is as follows:
Root directory: /index.php (splash page)
Subdirectory: /2015/index.php (wordpress installation with index.php)
When I click on any links on the homepage for the 2015 Wordpress installation it opens the index.php from the root instead of the index.php (splash page) inside the subdirectory, thus none of my links are working.
Both the root and 2015 folders have a Wordpress .htaccess file:
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress