The table which the core_0_1 update script uses seems to be setting the values backwards. For example it calls:
cursor.execute("UPDATE interpretation SET value=? WHERE value=?", r)
where r is equal to:
The first value in the tuple was what 0.3.3.1 uses, the second is what the new ontology uses. So it is converting the new ontology to the old ontology, which I imagine is not the desired effect.