When you encounter problems on the platform, its always a safe bet to restart the encode and see if that corrects the issue. Restarting allows the platform to reselect an instance and re-download the source, thus correcting any issues that may have arisen during the creation of the job.
Try these following steps to restart jobs:
..via UI: Select the job that has failed and choose from the drop down menu “Process”
..via API: use ProcessMedia to start jobs that already have tasks applied: http://www.encoding.com/when_should_i_use_the_processmedia_api_call
For API users, you can also use use UpdateMedia to add tasks: http://www.encoding.com/what_will_updatemedia_do_to_an_existing_mediaid