What tasks within your workflow could also be modifying the file? Make sure that any tasks that modify the file (setting attributes, submitting to Staging, etc) are owned by the person who initiated the workflow and not "system" or whatever user owns the task(s) currently.
Did you not develop your own workflows? I can't give you a crash course in workflow development. If you don't know where to look to see who owns a workflow task, you need more help than I can provide.