I managed to solve it doing the following: I tested most of free WooCommerce themes and none of them are compatible with this new version of the plugin. Every broke in somewhere.. So I removed the new updated version of WooCommerce plugin (2.01) and installed back again the old (1.6) and Mystile layout from my store back to normal. I did not lose any data, product or customization. Just had to put the pages in the top menu again, but it is easy via the custom menu. I had to do it in two stores from customers, but thank God it worked. Hope that helps someone. In any case, before to try this, do a backup.
Woothemes just came out with a new version of the Mystile theme today, it resolves most of the issues. There are still a few kinks to work out. Also, make sure the framework is updated as well. And if you have made any changes to the theme files, make sure to backup everything before upgrading the theme.
They should have upgraded their themes before they updated woocommerce to accommodate the changes.
You should download and install WP-PageNavi into your WordPress plugins directory and then activate the plugin in your WordPress Dashboard.
Once it is installed, you can set up the options using the settings page for this plugin in your WordPress Dashboard.
After you have the settings set up, add this code below to your current theme’s Functions.php file to have WP-PageNavi’s pagination replace WooCommerce’s default page navigation: