I'm having similar issues too. Or well I had similar issues at the beginning. Now, none of my lights work except for brake lights. I hope someone is able to answer your question and it is able to help me too.
At first, when I wiggled around my steering, it did that. Eventually, it led to me having to fumble with the wires through the side of my right fairing. And now it's completely black every time I start my bike. I have to wiggle the wires to get the lights on. Keep in mind, I'm riding an 06 R6S so our parts and stuff may vary.whelp, weirdest thing happened, drove the bike to work this morning, everything all buggy still, and as i pull in to park everything goes back to normal??? Sooooo yea i guess i'll just wait till that happens again and then take it to my local shop