A group of files takes a considerably longer time to process than if the are submitted individually to a workflow
Submit one file to Shuttle and it processes in about two minutes. Add similar files one at a time to Shuttle and they also process in about two minutes. Submit the group of files - six in this case - to Shuttle and it takes almost ninety minutes to process them.
The solution is to break the workflow into subworkflows (see screenshot below). Breaking a workflow into subworkflows breaks down the amount of information that one workflow has to process. In this case, the group of files complete processing in about two minutes compared to almost ninety minutes.