so, the round and flat pieces are two meshes. and, as I get it, you attached one to another.
remember that "smooth mesh" is not the same as "smoothing groups". I have that figured out since my headaches with milkshape
try aligning the edge of the flat pieces as close as posible to the border of the other piece, then cut a few poligons to create vertices that you can link with the flat part.
then, weld that section, and then smooth it out.
sort of this.