I actually don’t know what you want to achieve here. So let me point our few things you have done might have done wrong here.
1. If you want to just show the portfolio category you don’t need to use generic shortcode. From post type you can select the portfolio post type. And if taxonomy has been set to your post type, they will be listed while generating the shortcode.
2. The masonry layout seems working in the snapshot you sent to me. May be the chance that there are no images associated and you are using only image based layout. Have you tried to some other layouts ?
3. It really doesn’t make sense to use custom filters in functions.php unless you need custom query that our plugin doesn’t support via shortcode generation.
I am so sorry as the things you have done looks quite odd to me. So please check if the above mention things works for you. If you still have the issue, please let me know what you want to achieve and will try to guide as far as possible.