Because of the glitch, I am no longer able to import into Final Cut X. I have found a workaround. The import in Final Cut now only shows the primary Shared folder. So I'm copying what I need to import into that folder, importing from there, and then erasing the copy.
I'm sure Apple will update the glitch with a fix.
Other websites are now claiming that it is working as designed by Apple. If you have the newest version of iTunes and Find My Mac enabled it will hide /User at start up.
To stop it, uncheck Find My Mac, run the terminal script to show the folder and reboot. Turning Find My Mac back on will hide it again.
Still waiting for confirmation from Apple that this is the intended behavior.