You may not be doing anything wrong. Others here will know for sure and expand on this, but your S2000 mpu board has a socketed chip called the SG chip (Stepper Game) that controls a lot of these type options. There are different versions of these chips so your two S2000 machines may have different SG chips installed, hence the different options. The SG chip is not specific to your exact machine, it works in a variety of machines. The other socketed chip (SB chip) is the one that is game specific.
You may be able to replace your SG chip in the machine that isn't doing what you want and install a different compatible SG chip. There should be a label on top of the SG chip, you can compare the SG number on both machines. I think there is also a way to get into the Setup/Diagnostics and have the machine display the chip number on the front display.
One of the reasons there are different versions of SG chips has to do with gambling jurisdictions. In some places certain options are not allowed by law. Your 2 machines may have come from different jurisdictions. Or it may be because of what options or operating preferences the original casino that ordered the machine wanted. Or one of the machines may be a few years newer and that was the improved SG chip that they had started using by then.