distributor intermeadiate shaft?

The problem I'm trying to fix, is that when you put a timing light on the engine, it is way off. When you time the engine by ear, it runs fine. If you check the timing with a light after wards, it's way off. The only build problem is that this shaft was put in incorrectly and the wires relocated. Is it possible that this is upsetting the use of a timing light.
Thanks