The obligatory - how the libs work - so we all talk the same language:
Personally I have an extra hdd on my machine (but you could go with a separate partition on the same harddrive your program/os folder exists) where I keep all my user data.
I don’t keep data with the programs nor in a home or user folder.
Did you CHECK that 3d model in Freecad or some other tool to make sure it’s actually there and works?
Most models from parts manufacturers are way off the 0,0,0 position and will not show in KiCAD due to this.
You’d have to find their position and adjust it.. sorry.
And yeah, that’s why the people doing the KiCAD models put them at 0,0,0 oriented so there is no further messing needed in KiCAD, which then makes it look easy if one doesn’t know this 
What are the permissions/user you start(ed) KiCAD with and does this user have write access to to your home directory?