Yaesu G5500DC not engaging automatically - Arduino shield

Hello, our team has a Yaesu G-5500DC Az-El rotor, and we are using the following Arduino Shield setup to control the rotator through the external control port on the controller box.

Our problem is that when we activate the pin that pulls the corresponding wire on the DIN assembly low, (for example we activate pin 6, which is connected to the BJT on the shield that is connecting the R wire and the ground on the arduino when activated) the rotor does not start moving in the desired direction until we MANUALLY press the corresponding lever on the control box. After we press the lever the system goes in the desired direction. After the input is changed, the movement stops until we press the lever manually again. We would really like an automated system, and cannot figure out why this would be happening.

Any ideas?