Font Book says it's present, Fontexplorer says not.
The gist of the problem is right there. You should never have more than one font manager on your computer at a time. Assuming FEX is the one you prefer to use, you need to completely remove Font Book.
To remove Font Book from the hard drive, follow these steps:
1) Open Font Book, and then its preferences. Uncheck the box for "Alert me if system fonts change". Close the preferences and shut down Font Book. Put the Font Book application in the trash and delete it.
2) Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding it until OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally.
This will reset Font Book's database and clear the cache files in your user account. Any font sets you have created will be gone. Also, all fonts in the three main Fonts folders (System, Library, your user account) will now be active, regardless of their state beforehand. Not that what happens to Font Book's sets matter. We're removing it.
The main goal for the Safe Mode startup is to remove the orphaned Font Book database from the hard drive. With the Font Book application no longer on the hard drive, a new one cannot be created. Which is what we want.
3) Close
all running applications. From an administrator account, open the Terminal app and enter the following command. You can also copy/paste it from here into the Terminal window:
sudo atsutil databases -remove
This removes all font cache files. Both for the system and all user font cache files. After running the command, close Terminal and
immediately restart your Mac.