Hi Rafał,
I don’t see rel=”prettyPhoto” attribute added to your image links. It look’s like your product gallery is either published via custom gallery code (not based on WP gallery) or the filter we use to automatically modify image links is overriden (or removed) by the theme.
Can you take a look at how your product gallety is populated in a theme? If you find the code responsible for the display please try manually adding rel=”prettyPhoto[product-gallery]” to product image links.
Hope this helps.