If you found that your short codes are not working on your custom post types it is most likely due to an issue in how you are calling that post content on your theme.
Note that a plugin issue can be automatically discarded if your short codes are working on regular posts or pages as short codes are not dependent on the post type were you use them.
So as I was saying, this is very likely an issue in how you are calling your content which is not allowing WordPress to naturally expand short codes as it should.
For short codes to be properly expanded make sure you call your content as shown below:
<!--?php echo apply_filters( 'the_content', get_the_content() ) ?-->