It is a lot of hassle to get this to work for custom post types that are not typical. For example, if you have a custom post type with no menu in the sidebar, you won't be able to re-order the items. If you assign your custom post to "show in menu" under another menu, the re-order link won't appear, and for some reason it will give you permission errors.
It seems like a great plugin if it were only more developer friendly. If it had a function like...
"get_reorder_link( $post_type );"
Then I could just fix it myself.