theguy wrote: I've got products associated to a product category and to manufacturer category as well.
Hmmm, reads like you assigned the your products to manufacturer "categories" the same way as you assigned them to product categories. It's not intended this way, and then it won't work, of course.
In the product addition/edition page you have a dropdown for manufacturers/brands, where you can select one for each product. Then, once you set up a content menu or module, you can select the "Type of content" to be manufacturer/brand, so you'd get a listing of your manufacturers, from where you could then also show the products for a manufacturer, etc - all depending on the other settings for the listing.
So, both the category "manufacturer" assignments in the products and possibly also other categories you created directly under root are likely obsolete and can be removed, and it should all work fine.
In case of any more "malfunction" or confusion you might want to post screenshots of your configurations as it would help to see what you've done so far.