When selecting items, the CMS passes parameters to /index.php as part of the path. See AcceptPathInfo Directive
These parameters include ones that inform the CMS to run the shopping cart pages.
When you click Add To Cart, the same parameters are passed, but as POST parameters, and not as part of the path. So the URL in the address bar reflects the script handling the action only, /index.php
If you are getting what the CMS considers the "homepage" instead of the "shopping cart page", then the CMS is not getting passed parameters informing it to run the shopping cart.