Note that we don't officially support Compressor, as we've received many problem reports, and some of them resurfaced with recent updates – therefore, we suggest exporting directly from FCP or Motion.
More specifically, due to bugs introduced in Final Cut Pro 10.4.9, and later, and Apple Motion 5.4.6 (and later), the following actions may corrupt our plugins' registration on macOS:
Sending to Compressor (either from Final Cut or Motion),
Exporting MP4 from Motion,
Saving Motion projects with the “Save preview movie” option enabled.
To resolve the issue, please reinstall affected plugins using mInstaller - make sure that the newest version of the app is installed before doing so.
If you need to use Compressor, there's a workaround for FCP (not for Motion, though): open the File > Share > Add Destination dialog, and add a Compressor Settings destination. Thereafter, export your projects by selecting the newly added destination in the Share menu instead of using the Send to Compressor command.