I have seen this isue and it can arise when you export and import jobs for example between your live and your development repositories.
In effect the schedule then seems to run twice because, if the job exists on the live and development repository, it is executed from each repository, even though the schedule is only on the live. The easiest thing would be to delete the job from the development repository or perhaps even renaming may solve it.
We now avoid exporting and importing whole jobs - the highest level we will export at is at Workflow level.
Hope this helps someone.