You say there are two places to configure site profiles. As I understand it the site profiles are set up and configured in FTP Voyager; these profiles should then be available to be used by Scheduler. I can not see anywhere in Scheduler to maintain site profiles. I would have not thought this was a good thing to do in any case as that means profiles would have to be maintained in 2 different places.
As an example, I have created a new FTP site profile and stored it in the Personal Sites folder. When I go to Scheduler and create a new task I am asked to select the site profile to use; the Personal Sites folder is visible, but it is empty. This is the central problem I am having - the site profiles are not being made visible to Scheduler. I do recall that in an earlier version of Voyager the user had to specify profiles to be made available to Scheduler; again, I can not see any menu option or icon that will allow me to do this.