Motors change their direction after they are being disconnected and reconnected

[yifat]

Almost every time that we disconnect the electronics an connect it again, the motors change their direction. We have 2 motors in our driving system, when one is moving forwards and the other backwards (like the Pushbot) and a servo motor that is controlling the beacon arm position. In the code we set the direction of one of the motors to FORWARD and the other one to REVERSE, so that the robot will drive forwards and backwards appropriately. However, many times, after we disconnect the cables and connect them again, we see that the motors directions changes. Originally, we thought that we switched between the cables of the 2 motors, but we verified that this is not the case. We wrote a self-test that only activates one motor at a time and it seems that we control the correct motor. The power connectors of the motors do not allow you to switch between the positive and negative, so that connection is fine as well. We saw the same phenomenon with the servo motor. Before we touched its cables, it was turning left when we set its position to 0, but after we touched the connections, it is turning in the other direction, when we set it to the same position in the code. Again, all of the connectors of this motor are such that they can be connected in one direction only.
Did anyone ever saw such behavior? Any idea what can possibly cause it and how to avoid that?