Codecs, Codecs..... I've had a similar problem with conflicting MPEG codecs on some of my machines. What I sort of figured out is that NSV doesn't encode stuff right when it doesn't find the "right" codec.
My guess and it's just that is that NSV is picking the wrong codec for decoding. Check out your codecs and make sure that you don't have two that do the same thing. This seems to get easily confused.
Rule of thumb. Only install the codecs that you use. Nuke the rest.