When you turn the igniton on to pair the security system with your remote, wait until the turn signals flash once, indicating the security is disabled. Then turn the ignition off and the remote should pair with it once the two turn signal flashes indicate security enabled.
The 2013 FLHRSE5 Owners Manual is WRONG when it talks about turning the chirp on/off. The correct sequence is:
1. Turn ignition ON. Wait until red LED turns off, then turn ignition off.
2. Wait until the turn signals flash twice, then step 1. again.
3. Repeat 3 times. Then you should hear the chirp or if you were trying to turn the chirp off, the turn signals will flash without the chirp.
The above is only with the Smart Siren II (remote pager version).
Remember to use your Battery Tender when the bike with an alarm system is stored for 2 weeks or more.