Steam doesn't affect anything here. And it's installed wrong right now. The PF:CE Core Planets can be deleted, but should always be checked off when loading the game if you're doing that. And if you open KU2, you should find some folder with the names of the systems. Drop those in ~/KSP/GameData/PlanetFactory/PluginData/PlanetFactory/ Remove Barry, Stella and Serious, and it (hopefully) should work.