There is a setting in DocShuttle to "Display files newer than ?? days". By default, this settings is set to 120 days, so that any files older than 120 days are hidden. If the dictator is using a handheld recorder in which the date if off (e.g. if the battery has died), the date stamp on the files may be older than 120 days.
To check if this is the case, click "Tools | Settings" and change the "Display files newer than ?? days" setting to 5000. Then refresh the DocShuttle window and the hidden files will reappear.