(Totally agree about WP’s URL handling – massive pain).
Have tried all of those suggestions, but still having the issue. To elaborate:
1. The issue occurs when the permalinks are set to anything other than “Default”. (I’ve set them to “Month and name”, with a value for category base and tag base).
2. The issue is actually occurring with the default post type (ie not a custom post type). I’ve disabled all custom post types within the plugin and the issue still recurs. I can disable every component of Custom Content Type Manager and the issue recurs, but if I disable the plugin itself the issue fixes itself.
3. The issue also recurs regardless of the theme (I set the theme to “Twenty Eleven” and still had the same issue).
If it’s any help, the issue seems to have only begun occurring with the update to WP 3.5.1 (I’m on the current version of the Custom Content Type Manager plugin).
Thanks for your help so far!