In my fresh install of 4.0.4 only some of the “default” libraries are showing up in the library dialogs. I can manually add them through Preferences/component libraries. Specifically I noticed this on the MSP430 Library but others seem to be missing as well. I think my workaround of just adding everything in that folder seems to have solved my problem but I wonder if there is something I am missing as I am new to KiCad.
For global changes to stick you have to edit the kicad.pro project template file in
C:\Program Files\KiCad\share\kicad\template
It contains all symbol library links that will be part of any new project you start.
If you just want to do this for your current project you can use the Library Manager in EEschema or modify the .pro file in your project folder manually.
You can naturally use the Manager to adjust your current project file how you like it and then copy the relvant parts into the template project file.
example for my kicad.pro template file (note that the lib entries don’t have the .pretty extension):
…
[eeschema]
version=1
version=1
LibDir=E:/Data_KiCAD/_KiCAD_Symbols
[eeschema/libraries]
LibName1=.SchematicStuff
LibName2=Capacitors_0805_Kemet-16V-X7R
LibName3=Capacitors_0805_Kemet-50V-X7R
LibName4=Capacitors_1206_Kemet-50V-X7R
LibName5=Capacitors_Alu
LibName6=Con_Others
…