After upgrading to WordPress 3.9 some of my categories are not showing in category display.
MY set of plugins that are working with the new 3.9
Elegant Themes Updater
Find and replace
Global Content Blocks
Jetpack by WordPress.com
Orbisius Child Theme Creator
WPML CMS Nav
WPML Multilingual CMS
WPML Sticky Links
WPML String Translation
( WPML had issues with the new 3.9 but they have released a fix on their official site and it fixed my problem)
Yet Another Related Posts Plugin
All the plugins are up to date.
Now, I have tried just about everything and the problem keeps up repairing.
I made a fresh install on my local machine removed/deactivated all the plugins but the missing categories are not displaying untill i go and use the search.
It's not that big of a problem cause all the categories are reachable and can be wived when using the post/page editor search engine...
But, it's real annoying not being able to edit/see/browse through categories using category dashboard.
I did try with all plugins deactivated and with default WP theme and not even then the categories where not showing.
I have no time to go deeper in to code but as it looks this is a bug in new, all in all, great looking WordPress version.
So, if someone has the same problems and is looking for a solution and has some suggestions or fixes, please do post them here!