Custom Post Type UI – Categories not working properly with Custom Post Types

I’m using custom post types on my site and since I started using I seem to have lost the ability for categories to stay checked. I’m using Custom Post Type UI to manage them.

I’ve imported all my data using a CSV. The posts function fine if I don’t edit them. If I look at any of my posts I can see that nothing is selected as a category. If I select a category and save it the post will then become uncategorized. The original category is somewhere in the data, but is no longer showing up as a checkmark, so WP thinks it’s uncategorized.

Anyone have any idea what might be going amiss here?