I would suggest to enhance .htaccess a little bit.
My proposition:
# The following IF prevents "Error 500; Internal Server Error" if the server doesn't support rewriteBase.
<IfModule mod_rewrite.c>
AddType x-mapp-php5 .php
#AddHandler application/x-httpd-php5 .php
DirectoryIndex index.php
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_URI} ^(.*)//(.*)$
RewriteRule . %1/%2 [R=301,L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^.*$ index.php?qa-rewrite=$0&%{QUERY_STRING} [L]
</IfModule>
As long as RewriteBase should have always / as a value (even if the script is placed in some subfolder), "your-sub-folder" can be dropped.
Any more suggestions / upgrades ?