I got the same error when trying to "delete the database" and when "save changes to iTunes" was unchecked. I just tried the new version and got the same error. Now i am re emptying the database and I will report back when thats finished.
"Problem with delete duplicates: org.hibernate.exception.GenericJDBCException: The object is already closed [90007-172]
0 Duplicates found and deleted in 12,813 seconds"
the bizarre thing is that it clearly does find duplicates but will not delete them and acknowledge the dups it found