When my R6 had a bum battery, it would start and run just fine. I would shut it down and try to start it back and no dice. If I were to wait 20 mins, it would start right up. Dead/weak batteries do strange crap to bikes. It's the nature of these machines.
It's wise to invest in a battery tender and charger.
Now... I have to ask the obvious here, I see that you have installed leds. Did this problem start around the same time as that install? Might it be possible that the draw from the battery to power those are less than friendly to your battery in relation to your bike's ability to keep your battery properly charged? 2+2=4, See the relation? Turn your leds off and see if your battery keeps it charge.
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