The 'job manager' will only record jobs that have been scheduled (it reads its information from the Windows Scheduler). Saving a job/XML-file does not add anything to the job manger (it does not operate its own data storage but is only a 'filter' on top of the Windows Scheduler).
Am I correct that this is the issue or did I misunderstand? If so you are not the first person being confused about this and it also is a very old (and you could say rather primitive) implementation.