We had this issue, too, a while back when we made the transition. What we did was to add a "New Workflow Link" into the work flow where the files are stuck. This was used for files that were stuck in the wrong workflow since we had several different workflows. We limited the permissions to admin so no one else could use it. But it almost sounds like you are in just one workflow. If that is the case just give yourself permission to move the files or log in as admin and move them.
As for where a file starts in the workflow, there is a button on each of the states that says initial state. Which ever one you want to your process to start at is the one that should be selected.
Hope this helps;