Custom post type slug not working

I have two custom post types notes and programs, one custom taxonomy for them called subjects attached to them.

I want to achieve following:
For notes: http://site.com/%subject%/note/%postname% (http://site.com/data-structures/note/bubble-sort-algo)
For programs: http://site.com/%subject%/program/%postname% (http://site.com/programming-in-c/program/hello-world)

I’ve tried the plugin types and now using WCK for custom post types.
WCK Rewrite Slug: %subject%/note for notes and %subject%/program for programs.

In the Permalink Settings page, settings are as below:
common setting:
post name i.e. http://site.com/%postname%/
Permalink Setting for custom post type: (square braces are editable text input)
note – http://site.com/%subject%/note/%5B%postname%%5D
program – http://site.com/%subject%/program/%5B%postname%%5D

Now, http://site.com/data-structures/note/bubble-sort-algo and http://site.com/programming-in-c/program/hello-world are showing correctly but my main post are giving 404.

Whats the matter?

https://wordpress.org/plugins/custom-post-type-permalinks/