Hi Michael,
I am only horning in on this discussion because I am having this same problem. I have a complex file that originally suffered badly from the duplicated surface problem, with 1928 surfaces, and I have gone through and removed all the duplicated surfaces using v3 beta and, I thought, closed open joins. I have spent many many hours working to get it to a solid, but can't seem to get it to work. I am up against another deadline, so would appreciate you taking a look at it. May I send it along?

Best regards,
Bill Parker