I'm not sure, but this seems to be a bug inside the 'Enable multi entry from same user while form is persistent' functionality. In my opinion, the form should be cleared out when a user submits the form, so that a new entry can be made without using the old persistent data.
The 'persistent_multipage_forms.php' file contains a specific function that does the job. Provided with the correct $lead_id, the function 'delete_entry_from_gf_tables' removes all persistant data from the database. Maybe we could access this function directly and force a cleanup during a gform_submission_hook of some sort.