I don’t know if this problem is the theme problem or not, but when I change blog post permalink – this changes applies also to the products permalinks. Looks like products and blog posts have the same type.
For example: in general blog post settings I have this custom permalink structure: /blog/%category%/%postname%/ (by the way blog posts with this structure shows 404 error page and I don’t know why. you don’t know why?) and I have products custom permalink structure: /%product_cat%/product, but when I change the blog post permalink structure – Its also affects on the product permalink structure. For example: if I change blog post permalink structure to the default (?p=123) – products permalink structure also becomes the same.