I am having this same problem, actually--or perhaps it's only similar. I created my custom post types using functions.php, because I wanted greater control than plugins are currently offering. (I also don't want to have to deal with yet another plugin not being updated.)
In my case, I have four custom post types:
All of these work on the backend perfectly with their taxonomies, so I don't think there's an issue with the post types. Unfortunately, I cannot seem to assign custom field templates to multiple custom post types (no, I was not using a space after the comma), nor can I just duplicate the template and assign it to another post type.
I had a play around, and I discovered something strange. In functions.php, I've got my portfolio-artwork custom post type created first, followed by portfolio-photography. Now, if I make a custom field template for portfolio-artwork, it works, but I can never get one to work for any of the other post types that are created after it in functions.php.
However, if I switch one of the other post types to the top of functions.php, custom field template then works with it, but not the others. In other words, it's only recognizing the first created custom post type. It seems like there may be some issue with register_post_type being used more than once for custom field templates? I'm not sure. I don't see how using a plugin to create the post types would change this sort of issue, and I'd really rather not venture down that road.
Great plugin, but seriously hoping I can get this to work!