If you cups continuously go up and down when on power cycle.

1) Before doing anything else check your dip switch settings on the I/O board, if the issue started right after you change settings on the I/O board the issue is dip switch settings and you are in test mode.

2)  If issue started with no changes to the game then the issue is the ball position sensor. It is the three pin molex that goes to the sensor. The sensor is yellow in color and is square with ha red LED on it. The LED will come on when the sensor see the cup's cam gear off the motor. Just because the red LED comes on does not mean the sensor has sent a signal to the I/O board. 

3) To test the sensor you should see a voltage change or 5 volts when the motor's cam gear goes in front of the sensor. 

4) If you see the voltage change in the sensor then check continuity on the signal wire back to the I?O board.

5) If you have signal all the way back to the i/o board then change out the input chip that corresponds to the cup location in question.