Made a backup of the "Default" plugins then saving under a new name, start customizing.
"2018 Plugins"
 
The issue is in the Manager the folder structure and plugins all look correct.
In Track view, adding a plugin, almost none of the plugins are listed.
This is the same for all folders not just "Uncategorized"

Did you select the "layout" you want to use from the plug in layouts\manage layouts, at the very top?

Sadicus.
 
You just have to manually add the plugins back to their proper category manually.
 
Select the plugin manager and then select your particular custom plugin layout that you saved for yourself, (If you saved one)  Once you select it, Modify it to move the un-categorized plugins to their proper folders or make new folders and place the plugins in them accordingly.
 
Check out the video here ~~~> Sonar Plugin Manager for more Help
 
Good Luck

Thanks, I'll test it.
The problem is: plugins are added to folders (as shown in the image)  in Plugin Manager, and do not show in the Add FX list even if the correct folder is selected.