If the cold start lever was incorrectly installed, or the stop was bent, the cold start cam could go over center and apply a bit of advance when pushed backwards. I suspect lots of injection pumps behave in the same manner as yours. I wouldn't sweat it too much, the cold advance cam likely "finds" the point of least advance during operation due to engine vibration and spring pressure from the advance mechanism. You probably should have left it there while timing it, instead of pushing it all the way back.
Thats probably the best approach for the time being. Of course the "proper" thing to do would be to pull the pump off the engine, lock the pump pulley somewhere on the rising edge of an injection stroke, install the timing guage and set the adjustable stop on the cold start advance so that it stops the lever at the point of least advance. Not fun...