If the S4R electrics are the same as my old S2R, then I think you have to pair the new clocks with the ECU using the red key. I'm afraid I don't know the actual procedure, maybe another S4R owner will chip in with some more information.
Alternatively, you could try asking Avanti Racing for advice or help.
http://www.avantiraceparts.co.uk/page.php?id=19