My FI light flashes quite often but it always resets with the ignition, and nothing appears when I try to read the code.
It nearly always happens if I cruise for a couple of miles at the point where the vibration is worst. Like the original poster said, there's no effect on performance while it's flashing. Mine is a 2010 Z1000.
2010 Z1000 Akrapovic 4 into 2, Maxton revalved/resprung forks and rear shock with remote reservoir, Ivans ecu and block-off plates, Rizoma bars, PCV, Lightweight battery, R&G fender eliminator and sliders, HEL stainless brake lines, Galfer rear rotor, HyperPro steering damper, Active q/a throttle, Ninja 1000 SX wheels.