I recently had this precise issue with a later version of Motion — 5.3.2. I first noticed it because 3rd party plugins were not working properly in FCPX. I took a suggestion I found online, and tried opening the plugins in Motion, where I got the message that filters AND generators were missing. I believe this happened around the time I updated to supplemental Motion content 1.1, but that's just an observation. I spent a week reinstalling, disconnecting hard drives, trashing preferences, the whole nine yards. Nothing worked. Nothing. Then I spent the better part of a morning on the phone with Apple support. Again, zip. Then I decided that before doing a clean reinstall of the system (what a humongous pain in the tush that is), I would try to downgrade to an earlier version of Motion. I found a copy of 5.2 on a Time Machine drive I had disconnected — and voila! All missing generators and filters miraculously reappeared, and everything in Motion and Final Cut Pro started working fine again. With all due respect, for some users, the newest version of Motion (5.3.2) and/or its supplemental content, is just not working right. Find yourself an earlier iteration of the app, and I am betting your sorrows will soon be over. (For what it is worth, I am running El Capitan on a 2013 Mac Pro (the black trashcan model).
