Permalinks and cart go wrong

Hello.
Yesterday we had a problem with cart in MarketPress on WP 3.4.2. Hoping in a lucky solution we tried installing the 3.5 version from scratch and reinstalling all plugins, lasting with MarketPress which ask for pretty permalinks.
After that, something is going wrong!
Now there are 2 problems:
1) pages and articles don't redirect correctly to their URL; MarketPress links are formed without "index.php";
2) cart doesn't work yet; it seems accepting items, but on reload some itemps disappear.
We are going crazy!

Site URL is http://www.cromamultimedia.com (sorry, it's an Italian site) and the shop would be at http://www.cromamultimedia.com/store... but its at http://www.cromamultimedia.com/index.php/store

Thank you in advance for your help.

Alf & Massimo