This issue is addressed in Final Cut Pro X 10.0.3, Motion 5.0.2, and Compressor 4.0.2.
Final Cut Pro X, Motion 5, Compressor 4: Custom/duplicate Compressor settings may not be preserved
Custom settings or duplicates of existing settings created in Compressor may not be preserved. This can occur if right after using Share > Send to Compressor from Final Cut Pro X or Motion 5, you create the settings, quit Compressor, and then quit the app that sent the project to Compressor (Final Cut Pro X or Motion 5).
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