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).
Compressor 4, Motion 5, Final Cut Pro X
To workaround this issue, quit the app that was used to send the project to Compressor (Final Cut Pro X or Motion 5) before quitting Compressor.
Alternately, you can create a custom setting in Compressor prior to sending the project from Final Cut Pro X or Motion.