I am afraid that there is no way to fix the offset that I know of. Since it is an iso view, it breaks where you sktech and moves them closer at those breaks. It is just the nature of the beast.
Sachin - your part had the same problem. If you break a part it will not follow the angle, it only moves the 2 pieces together horizontally. Picture your part on a piece of paper. draw 2 vertical lines for the break. Now fold the paper over to where the 2 vertical lines meet. That is what the break command does. Break is good for long straight parts.