Something is still offline. You could look in the browser and see if you see a red offline sign, or select the library and choose File > Relink Files and select the radio button to "missing" and see if X reports which files are still missing.
I have seen the the Offline indicator on my setup with all media connected - it turned out to be a missing transition. I'd been cleaning up my effects / transitions / generators (removing demos, etc.), and I had inadvertently left a demo transition in one of my projects.
Maybe try to consolidate the media in your location of choice - even though it's there already. This time letting FC complete the task rather than doing it in the finder. Another possibility is to delete preferences.
Reset preferences in Final Cut Pro X 10.1.2 or later
Quit Final Cut Pro X.
Hold down the Command and Option keys while reopening Final Cut Pro X. A window will appear asking "Do you want to delete preferences?"
or sometimes just rebooting computer does the trick.
Mac Pro, macbook pro, Imacs (i7); Canon 5D Mark III/70D, Panasonic AG-HPX170/AG-HPX250P, Canon HV40, Sony Z7U/VX2000/PD170; FCP 6 certified; FCP X write professionally for a variety of media; teach video production in L.A.