here is what's happening and the probable solution and NO....the "auto spark plug/combustion chamber clearing" process is not being initiated on its own. impossible! the event you described was a partial combustion process with the fumes from combustion blowing out the intake valve and up thru the TB eventually into atmosphere...hence the aroma and sound.
1-auto clearing feature can only be achieved by holding throttle wide open....placing red run switch to on position...and then turning on the key. if you are NOT doing this the auto feature will NOT activate
2-occasionally when you shut off the motor the intake valve in one and only one cylinder remains partially open. a random occurrence. unspent fuel droplets then form a combustible vapor in that cylinder and remain there for a period of time. that amount of time dependent on tons of variables.
3-you now proceed to start the bike with the above random conditions in place and hear a "pop or poof" as you described it coming from the airbox area in conjunction with combustion aroma....perhaps even a wisp of smoke.
4-how did this happen? simply put your coil fired. it is a "dual-fire" design. why did this happen? it found a ground source and activated itself firing both plugs and causing this event.
the solution? start checking all your grounds. i've listed the 2008 ulysses grounds on here 25X or more. YOU HAVE AN INADEQUATE AND/OR BAD GROUND. simple as that.