Basic and the most important configuration section of pretty clean urls is located on module configuration page. Here you can control from what pages module will remove the ID. PrestaShop has several types of pages and each of these pages can have ID or not, for example: category pages, product pages, cms pages, cms category pages, suppliers, manufacturers.
Screenshot above shows how the module configuration looks like. As you can see - there is several positions. You can enable or disable these options. If some from these optons will be enabled - module will remove the ID from the url. If you will disable these options - module will not remove the ID.
If you run shops with multistore environment there is a chance that you will have define settings of the module for each available shop in your back office. In this case while you will edit the module please select shop that you want to configure from shop-context menu. Verify settings for each shop.