Upon further investigation. I think I have narrowed the problem down to the linear scale on the Y2 axis. While the operators manuals doesn't go into detail I spoke with an Amada tech that told me it first slightly moves the Y axis down to sense the position and then initiates the back-gauge. Without a signal telling it the Y axis is moving it will continue to try and move the cylinder. So I Found the connections for the linear scales, swapped the Y1 and Y2 and the problem switched sides. Which in my mind says the board, and relays are working properly since it now thinks the missing reading is on the Y1 axis. I tried taking it apart and cleaning the glass and reader, but it did not fix the problem. So I have another one on the way that should arrive tomorrow. I will update the thread if it fixes the problem.