Magento 1.8 – Multiple Websites in Subfolders

I am using Magento 1.8.1.0 with multiple websites.
I followed the instructions to setup the multiple websites as described here: http://www.dbits.be/blog/index.php/How-To/magento-multi-store-setup-sub-folders.html

• Create stores/views/sites
• Set default URL (safe/unsafe) and Homepage for each store.
• Create subfolders, files & symlinks
• Edit index.php in each subfolder

I would say that my setup is working halfway:

www.mydomain.com/ is pointing to my base website. This website is working perfectly fine.

www.mydomain.com/paris/ is pointing to the Paris website homepage which is fine. The links in the menu all have the www.mydomain.com/paris/ subfolder part, so this seems to be working fine too.

Problem is when I try to access a category or a product within a secondary website, such as www.mydomain.com/paris/shirts/

This type of URL is redirecting to the main website homepage. So it seems Magento doesn't recognize urls of type www.mydomain.com/paris/xxxx to belong to the Paris website but is looking in the base website, can't find anything and redirects to the base website's homepage.

I am out of ideas on how to fix this, any suggestion would be highly appreciated.