Isometric perspective is orthographic after all so all curves and things placed at an angle will always look weird if you stare at it for too long. I've been making iso houses for a game concept and the roofs always look kooky. Even if I follow the rules everything looks completely weird if I look at it closely. On the other hand, if I just leave it and view it as part of the big picture, it'll feel just fine.
Just a tip is, don't strive for a feeling of absolute perfection - with iso it's more that if you follow the rules of the perspective you can be happy with yourself. Strive for knowing that you did it perfect, because in iso, even perfect looks weird to the human eye.