That's a good question. When I read blackmetoc's post I did some reading. It seems that an unhealthy battery can result in poor spark plug performance and a heavier load on the alternator / motor, and poor injector performance to name 3 issues that might result in change to fuel economy. Hell, maybe crappy gas or easing up on the throttle is the answer. But...modern bikes depend almost entirely if not completely on electronics to run efficiently, so these things makes sense to me.
*blackmetoc Let us know what you find your issue to be.