G-Code can recognize a comma, that is why it should not be used with the S command
What is the spindle motor you are using as not all can have FWD and Reverse??
Do you have this manual??
The Ports & Pins Outputs for the spindle control can be set to active low, just depends on the configuration, doing this has nothing to do with Step / Dir control
Have you checked all the jumpers on the MB3 Board are in the right position.