Limitations of working with projects.
Please note: The current version of Scribeomatic will only transcribe audio in the primary storyline when a project is transcribed. To workaround this you may wish to export a master clip of your timeline then you can drag that from the finder into Scribeomatic and transcribe.
The resulting transcription of the project can then be re-imported into FCP X if needed. Additional details on the best methods of doing that will be added here shortly.