Hello, I am running into the same issue on my installation. I am trying to add multiple custom taxonomies, and I am seeing the same issue that Dadastudio describes
1. I select a custom taxonomies and click Update Media
2. I go back to Edit Media screen
3. Checkboxes are not selected.
In my functions.php file I am using the new object oriented method like so:
$wood_species_metabox = new Media_Categories('wood_species');
$wood_installation_metabox = new Media_Categories('wood_installation');
Any ideas?