Try enabling Collect Job Documents on the Print component.
From the FreeFlow Core Help Guide:
To submit jobs to the DFE in the order defined in the Job Group Sequence Behavior, the Print component enables the Collect Job Documents option.
Job Group Sequence Behavior The sequence of jobs in a Job Group is based on the following: • Submit Job: Jobs are sequenced in the order in which they appear in the Submit Job Dialog Document List. • Manifest Jobs: Jobs are sequenced in the order in which they appear within the Manifest. Refer to: Manifest Automation from Xerox Setup. • JMF Jobs: Jobs are sequenced in the order in which they appear within the Run List in the JDF submitted during Job Group Sequence Behavior. • Zip files: Jobs are sequenced alphabetically based on their filenames. • Split Jobs: When splitting a job, the resultant jobs are sequenced based on the order of the Rules table in the Split component. • Split jobs in a job group: When splitting a jobs in a job group, additional jobs are sequenced based on the order of the Rules table in the split component. In addition, these additional jobs are sequenced after the job from which the additional job was created.