Did you use 4.0.x before you upgraded to nightly builds? There may be some configuration problems. If you don’t use v4 anymore you can delete the config directory, ~/.config/kicad and start from scratch. If you want to keep the possibility to continue with v4 I recommend using different environment variables for v5. See Any ultimate Guide on how to use KiCad 4 and 5 on one System?.
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