I doubt it will make a difference if you rotate the shaft as the motor/gearbox does not have a 'home' position, as Dave stated the switch activation lets the game know what postion the gumball it in.  Is the motor running in the correct direction? sounds wierd that you can load up all the slots of the seperator without even dispensing one ball.

You could be right Matt, that's one thing I thought about lying in bed. I think it is but can't be sure. At the moment the seperator that has 4 holes can have 3 of the holes loaded with balls so maybe its going the wrong way. I wired as per the old motor but whats saying the lugs/motor isn't mounted 180 degrees out.

Will have to look at this tonight and see which way the seperator rotates and get to you guys. I'm confident this isn't a major probkem.