I am assuming you mean that when the spindle brake is Released in the auto mode, the spindle motor feels active at zero speed? And the machine has a Spindle-Free switch or something to put it in this mode in other functions.
Number one it seems that the spindle is kept ON at zero speed as a C axis would.
The functions to do this is usually done in the ladder PMC and I cannot think of a parameter that might do this. Are you sure there is not an M code that would turn this situation off?