XF 2.3 index.php in other folders issue

[jtorral]

Let's assume the following:

www.example.com

Is my xenforo base. Everything works there

However, if I put my own app with its own index.php in

www.example.com/myapp/index.php

Xenforo freeks out and does not allow it.

My existing htaccess in xenforo root is as follow

ErrorDocument 401 default
ErrorDocument 403 default
ErrorDocument 404 default
ErrorDocument 405 default
ErrorDocument 406 default
ErrorDocument 500 default
ErrorDocument 501 default
ErrorDocument 503 default

<IfModule mod_rewrite.c>
        RewriteEngine On
        RewriteRule ^node/(.*)$ /threads/$1 [NC,L]

        #       If you are having problems with the rewrite rules, remove the "#" from the
        #       line that begins "RewriteBase" below. You will also have to change the path
        #       of the rewrite to reflect the path to your XenForo installation.
        #RewriteBase /xenforo

        #       This line may be needed to workaround HTTP Basic auth issues when using PHP as a CGI.
        #RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization}]

        RewriteCond %{REQUEST_FILENAME} -f [OR]
        RewriteCond %{REQUEST_FILENAME} -l [OR]
        RewriteCond %{REQUEST_FILENAME} -d
        RewriteRule ^.*$ - [NC,L]
        RewriteRule ^(data/|js/|styles/|install/|favicon\.ico|crossdomain\.xml|robots\.txt) - [NC,L]
        RewriteRule ^.*$ index.php [NC,L]
</IfModule>

And the rewrite for index.php has no affect on my issue wheter i leave it or comment it out.

Is there something I am missing ?

Thanks!

JT