Hi Paul,
That behavior certainly looks odd. From what I've seen, I suspect the vectors in .sspace file have NaN values, which is why you're seeing NaN similarities. However, I'm not sure why exactly the vectors have those values. Given that you're using the HEAD version, it should be selecting SVDLIBJ for the SVD operation, which should give stable results. I just tested the trunk on our end and it seems to produce reasonable results, so perhaps it's something specific to your corpus, or to your system. How big is the corpus you are using? If we can't figure the issue out by email, would you be willing to run custom LSA jar with lots of debug output so we could track what's going on internally?
Thanks,
David