The only other thought I had is that maybe the bike is throwing you an error code. Check all your bulbs first, but maybe it may wind up being an issue to be fixed under warranty.
Sounds like you've got a pinched wire in the switch housing. Maybe wires got pinched together and a turn signal when it flashes is powering your ignition or something. If that happens the current draw might not let the security system be satisfied, and it might continually go off.
I have a friend that has a 2010 fatboy lo. His lights started going crazy. Happened mainly when he was running but it did it a couple times when it was shut off. Dealer thought it was the security module. Turns out the wiring that runs from back under the fender to the tail lights is no longer run through clips under the fender. They have it in a tube with double stick tape. Of course after riding in rain, and the big time heat it dropped down and the tire rubbed off the protective tube and the insulation on the wires creating shorts. Maybe check for that too.