Thanks to all for your comments. Glad you like the house - it's weird talking about content rather than process on this site! And thanks for the comment on the non-seismic decks. You are certainly right; they'rer still schematic at this point - I'm meeting with my engineer Friday to firm everything up.
As for the anomaly issues, we're still batting zero. As regards the mismatch between VW and OS 10.3.9, (I've now also gone to 10.4.2), I tried opening it with Classic, and Classic just doesn't see it. I've been using VW 10.1 for a couple of years, and have never seen anything like this.
I tried Erich's suggested procedure, and got the same anomaly. Usually, I just use the walk-through and flyover tools, but even with set 3D view, the house still goes missing from certain directions. I've looked through what I think are all the linked layers for some weird item that could be causing this glitch, but I can't find it. But as I said, I've got another linked model that is working just fine, and hopefully I'll never see this problem show up again.
Thanks again.