When I learned better to use a grain plate, I tested this method with EFNY too, and I noted that the quality is quite better with it applied, thing that I haven't done at the time of project release... grain helps to hide the small artifacts present in the HDTV source, without over processing - DNR in particular...
If all my other projects are OK, maybe there was some sort of problem during the authoring; as V1.1 will involve a complete new encoding, I hope compatibility problems will not arise with it...