Use case: (see also https://drupal.org/node/1216224#comment-7477170)
Create a filter format
Create a ckeditor profile (or modify an existing one) that is assigned to the above format
Export both of these things to a feature
Enable the feature on a clean install
The ckeditor profile is imported, but it no longer has the assignment to it's input format. That is because if the format does not exist when the ckeditor profile is created, the ckeditor_input_format row is removed from the db. If the format does exist, it's fine.
Current workaround is to maintain two features - one with the input format, the other with the ckeditor profile - and use module dependencies to ensure the correct order.