Paul is this a Revision 3.xx scope? If so, I don't believe the hand controller knows which way the N/S switch is set. It does not send tracking information to the telescope either, so I don't feel it could be sending erroneous information that would cause the scope to change direction.
In the period before you start pressing keys on the hand controller's keypad, it sends no information to the telescope other than its 4-byte "wake up" message, which is always the same. Before the wake up message, the scope sends no information to the hand controller, so the hand controller could not know about the N/S switch before sending its only message to the scope (which is always the same anyway).
After the wake up message, some data comes from the telescope to the hand controller, but if you have not pressed any keys, the hand controller has sent nothing back the other way. Also, the data sent by the telescope at that time is identical whichever way the N/S switch is set, so the hand controller is ignorant of that setting.
Again, this is all for a revision 3 scope only.