Permalinks not working - Githubissues

Please make sure you are including enough information to make this a valid
bug report: https://code.google.com/p/wordpress-custom-content-type-
manager/wiki/ReportingBugs

*SYSTEM INFO* 
------------------------ 
Plugin Version: 0.9.7.11-pl
WordPress Version: 3.8
PHP Version: 5.4.23
MySQL Version: 5.5.32-cll-lve
Server OS: Linux
Language: 
------------------------ 
ACTIVE PLUGINS: 
 * ARYO Activity Log v.1.0.8 [http://wordpress.org/plugins/aryo-activity-log/]
 * Auto-Schedule Posts v.3.6 [http://plugins.davidjmiller.org/auto-schedule-posts/]
 * BuddyPress Custom Profile Menu v.1.3.4 [http://sensibleplugins.com/]
 * BuddyPress Group-O-Matic v.1.0.4 [http://community.presscrew.com/]
 * BuddyPress login redirect v.2.1 [http://www.appinstore.com/buddypress-login-redirect/]
 * BuddyPress Toolbar v.1.6.0 [http://genesisthemes.de/en/wp-plugins/buddypress-toolbar/]
 * Buddypress Xprofile Custom Fields Type v.1.5.8.3 [https://github.com/donmik/buddypress-xprofile-custom-fields-type/]
 * BuddyPress v.1.9.1 [http://buddypress.org]
 * Category Post list Widget v.1.1 []
 * ClickDesk Live Chat, Help Desk & Voice Chat v.4.2 [http://www.clickdesk.com]
 * Contact Form 7 v.3.6 [http://contactform7.com/]
 * CubePoints Buddypress Integration v.1.9.8.9 [http://wordpress.org/extend/plugins/cubepoints-buddypress-integration/]
 * CubePoints v.3.2.1 [http://cubepoints.com]
 * Google Analytics for WordPress v.4.3.3 [http://yoast.com/wordpress/google-analytics/#utm_source=wordpress&utm_medium=plugin&utm_campaign=wpgaplugin&utm_content=v420]
 * Google XML Sitemaps v.3.4 [http://www.arnebrachhold.de/redir/sitemap-home/]
 * Hit Sniffer Live Blog Analytics v.2.8.4.3 [http://www.hitsniffer.com/]
 * Jetpack by WordPress.com v.2.7 [http://wordpress.org/extend/plugins/jetpack/]
 * List category posts v.0.39 [https://github.com/picandocodigo/List-Category-Posts]
 * Membership v.3.4.4.1 [http://premium.wpmudev.org/project/membership]
 * Social Login v.4.4 [http://www.oneall.com/]
 * Post Lists View Custom v.1.5.5 [http://wordpress.org/extend/plugins/post-lists-view-custom/]
 * Regenerate Thumbnails v.2.2.4 [http://www.viper007bond.com/wordpress-plugins/regenerate-thumbnails/]
 * Responsive Lightbox v.1.3.2 [http://www.dfactory.eu/plugins/responsive-lightbox/]
 * Rewrite Rules Inspector v.1.2.1 [http://wordpress.org/extend/plugins/rewrite-rules-inspector/]
 * Search & Filter v.1.1.2 [http://www.designsandcode.com/447/wordpress-search-filter-plugin-for-taxonomies/]
 * SortTable Post v.4.2 [http://mynewsitepreview.com/sorttablepost]
 * SEO Plugin by SQUIRRLY v.2.1.7 [https://my.squirrly.co]
 * Sweet Captcha v.3.0.6 [http://www.sweetcaptcha.com]
 * Trackable Social Share Icons v.1.3 [http://www.ecreativeim.com/trackable-social-share-icons]
 * Tracking Code v.1.1 [http://wordpress.org/extend/plugins/tracking-code]
 * WordPress SEO v.1.4.22 [http://yoast.com/wordpress/seo/#utm_source=wpadmin&utm_medium=plugin&utm_campaign=wpseoplugin]
 * WP Analytics Tracking v.1.0.2 [http://neoptin.com/]
 * WP Changes Tracker v.2.0.3 [http://pixeline.be]
 * WP-PageNavi v.2.83 [http://wordpress.org/extend/plugins/wp-pagenavi/]
 * Video Manual for WordPress SEO by Yoast v.1.0.2 [http://yoast.com/wordpress/seo-video-manual/]
------------------------ 
CURRENT THEME: Hueman v.1.2.4 http://alxmedia.se/themes/hueman/

What steps will reproduce the problem? (Be *specific*)
1. Permalinks are set to Custom.../%category%/%postname%/

What is the expected output?
Access the custom Post type from the menu, e.g. 
http://www.101businessinsights.info/books/predictive-analytics-microsoft-excel/

In the link above the Custom Post Type is being used in the permalink instead 
of the Category. E.g. the Custom Post type in this example is books, whereas 
the category is Business Tools

What do you see instead?

404 Page not found.

Does the problem continue if you disable all other plugins? (plugin
conflicts cause a LOT of problems, so please isolate the problem)

The page is visible if I use the default permalink option, e.g. just the page 
number.

Please copy and paste the system information that appears in a yellow
textarea when you click on "Report a Bug" on any CCTM admin screen (this
includes the version of the
plugin, the version of PHP, the version of MySQL, a list of other active
plugins etc.):
Original issue reported on code.google.com by andrew...@gmail.com on 4 Jan 2014 at 3:28
Merged into: #534
MammothMKIV / wordpress-custom-content-type-manager

Permalinks not working #538
