I believe I had a similar issue. My problem was bad wall cleanups. It was user carelessness, but because of the cleanup issue everything would disappear in 3D. You can tell if it is an issue by looking at your model in 3D ISO (parallel) view. If it shows up at any zoom level, then you might have a cleanup error. If this is the case, use the marquee to isolate different sections in 3D and narrow your search down to what walls are not cleaning up.
