Might it be that you had a late nightly running instead of the stable version of kicad 4? This would explain why there is a atmel lib (such a lib does not exist in version 5)
You might want to delete the sym-lib-table and fp-lib-table files found in your config directory and let kicad setup its defaults.
Using the library managers you can add more than one lib at a time. Leftclick on on lib and shift plus leftclick on another lib (everything in between will also be selected) For finer control use crtl plus leftclick.