It's possible that you have a bad battery. Most ECM's (computers) use 5v references for all of the machines on board sensors. If the battery voltage drops below 11 voltsit may still crank the bike but, while cranking you generally will drop 1 to 1 1/2 volts. When this happens and the voltage drops there wouldn't be enough to keep the 5v reference for the computer. Without the reference the computer won't see the crank sense and the FI will not fire. I'm an auto mechanic but the FI bikes these days use the same setup that your car uses. I have seen this happen with cars. One thing to remember with computer controlled engines also is, NEVER boost them to jump start them. In other words, you can use a jump pack or charge the battery but don't use a battery charger that has a boost option for starting. It force feeds the battery and therefore all the electrical components including the ECM and sensors. You can damage the ECM, ignition module, stator or cranksensor(whichever setup your bike may have).
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