Have you set up the permailinks in Wordpress so your .htaccess looks like the following?;
# 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
The line RewriteCond %{REQUEST_FILENAME} !-d
is telling the server not to include rewrites for directories which are in the root of the install, so anything within your shop directory shouldn't be processed through index.php
.