WooCommerce Permalinks broken (wrong prefix)

Hi,

I just tried out the plugin, saw it was the right solution for my problem. So I purchased the pro version so that i could also select the product_cat to use for the product permalink. But now all permalinks to products are broken. Instead of /shop/%product_cat%/%product% the permalink starts with /wp. So its /wp/shop/%product_cat%/%product% instead of /shop/%product_cat%/%product%.

Could you please help?

I have WordPress 4.7.3 with WooCommerce 2.6.14 and wp-category-permalink 3.2.6 running on a root.io/sage theme.

The plugins page states the followig about custom post type taxonomies, that are supported:

Permalink: /shop/%product_cat%/%product%
Post Type: product
Taxonomies: product_cat pa_format pa_sex pa_size

Thanks in advance for your help,
Matthias