I have gone through my old NEQ6 manual and other than the co-ordinate S designator i can't see what else you need to do. Is this a brand new, never used before mount?
I agree that trying another hand controller is a good idea, or you could use Sky Safari as it has avprofile for that mount, but you would need a wifi box like a Nexus to connect to the bottom of the controller.
Sounds like a call to Bintel might be in order.
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