EZWire1616 is controlled by the SmartTILE-Fx CPU which is the same as that on Fx2424 and Fx1616-BA.
The default stepper motor channels for STEPPER 2 is indeed Outputs 9 & 10. If you run a function that comprises only the following two lines:
STEPSPEED 2,100,10
STEPMOVE 2, 5000, 5
You should observe that the pulse are sent out of the output 10. If you run negative pulses then the direction signal will turn on Output #9.
SmartTILE-Fx does support 3 stepper channel so EZwire1616 should support 3 stepper channels as well.
When Fx1616-BA was released, there were only 4 high speed digital outputs 5 to 8 as all the other outputs are all relays. To support application that may want to use two stepper channel, we provided a special way of using output 7 & 8 as pulse and directional output for STEPPER #2. However, this is only activated when you run the stepper using
STEPMOVE 32, count, relay#
I wonder if you have accidentally run the above command and thus observing stepper output on 7 & 8?