This should not be a problem (assuming Soundbite is successfully indexing the MOV files). A couple of points to consider:
— First, are you actually creating a new sub-clip or clip – i.e., an indexable asset on disk — or by “link the clips together”, are you creating some form of virtual asset in the project that is not actually a media file on disk?
— At what point are you adding the project to Soundbite? When it’s added, are the MOV files present or just the WAV’s? If the MOV files are added to the project after adding the project to Soundbite, it may need to be “refreshed”. Once you save changes to a project, Soundbite will recognize that it is not in sync and notify you.
— If the project contains a new physical media file that you’d like markers for and Soundbite doesnt appear to recognize that file, then the file itself could be a problem. Is the file encoded with anything proprietary that requires a special codec or is it simply a QT MOV file?