I've got a custom post type set up - "Webinar" - and a whole bunch of categories with subcategories. Now, in the master category list all the categories are listed correctly with their subcategories indented under them. But on the add/edit a Webinar page, the list of category checkboxes isn't quite right: for one particular category, the subcategories aren't listed below it. They're all right at the bottom of the list, and not indented, like they're parent categories. This is only for one category - the others are all listed correctly. And even weirder, when you do tick one of the errant subcategories and update the post, it gets moved to its correct place under the parent category.
I don't know what the cause might be. Incorrect parent ID's in the database was my first thought, but then it's displaying correctly in the master list. I don't know enough about WP's database structure to confirm.