Some further testing has revealed that if i take one ball out (ie: only 5 installed) the machine only loads one ball into the shooter lane - the game works fine until it tries to use a ball stored under the playfield for a mode such as battle simulation - then it gets confused as there are only five balls instead of six.

So this sort of points back to the trough being the problem, yet when i put my indy trough boards in it still showed the same problems. 

As this game stores 2 balls under the playfield, i guess if there were any suspect optos they would be number 3 or 4 in the trough (as there are only ever 4 balls in the trough)???????????