I think this is a problem with a new version of jetpack. I tried it with an older version (0.93) of custom permalinks yesterday and I got the same problems. I had no problems with this version several weeks before.
I disabled the extra-widgets of jetpack and all works fine.
The problem is, after updating a post or category, jetpack adds two entries in the custom permalink list: widget_image, Jetpack_migration, permalink (of the updated post or category) and sidebars_widgets, Jetpack_migration, permalink (of the updated post or category). The post or category custom-permalink doesn’t work. After deleting both jetpack-entries in the custom permalink list the post or category custom-permalink works.
