This seems to be a software glitch in the new 5.9 ECU (Ignition/Fuel Injection Box). My '02 S4 has done it a couple of times, other folks with '02 and later Monsters seem to have it happen occasionally.
It hasn't amounted to anything more than an annoyance for me, and nobody has reported any trouble from this issue.
Just FYI, when you push the start button, you are 'asking' the ECU to start the bike. It looks at all of the sensors, and decides whether it will start the bike or not. Apparently, it gets confused occasionally. Just 'reboot' with the key as you have been doing.