i think i can relate to your problem. I use Nurbs for Stereo Lith so it needs to be a good mesh. what you need to do is make sure that both the isoparms or curves that you are using have the same number of CV's then, after you create the fillet, use stitch edge tool. MtMckinley has a great shark tutorial to get you used to this process. watch it. He uses Global stich to finsish it off with great results.