Please try disconnecting all motors and just measuring the voltage difference between the two pairs of driver pins. Do you get the results you would expect when you turn the pot?
I am not sure why one of the channels works while the other doesn’t, but I suspect that problem is with your power supply. As it says in the announcement at the top of this forum, 9V batteries are not generally strong enough to drive motors. If the Baby Orangutan behaves as expected when the motors are disconnected, then the problem is almost certainly with your power supply.
If the motor draws too much current from your battery, the battery voltage will drop and cause the Baby Orangutan to reset. You can use the LED on the Baby Orangutan to debug this further: if you program it to blink a few times on startup before driving the motor then you can tell whenever the Baby Orangutan is getting reset.
–David